Delta-8 desaturases and their use in making polyunsaturated fatty acids

ABSTRACT

Isolated nucleic acid fragments and recombinant constructs comprising such fragments encoding delta-8 desaturases along with a method of making long-chain polyunsaturated fatty acids (PUFAs) and using these delta-8 desaturases in plants.

This application claims the benefit of U.S. Provisional PatentApplication No. 60/910,831, filed Apr. 10, 2007, the entire content ofwhich is hereby incorporated by reference.

FIELD OF THE INVENTION

This invention is in the field of biotechnology. More specifically, thisinvention pertains to polynucleotide sequences encoding delta-8desaturases and the use of these desaturases in making long-chainpolyunsaturated fatty acids (PUFAs).

BACKGROUND OF THE INVENTION

The importance of PUFAs is undisputed. For example, certain PUFAs areimportant biological components of healthy cells and are recognized as:“essential” fatty acids that cannot be synthesized de novo in mammalsand instead must be obtained either in the diet or derived by furtherelongation and desaturation of linoleic acid (LA; 18:2 ω-6) orα-linolenic acid (ALA; 18:3 ω-3); constituents of plasma membranes ofcells, where they may be found in such forms as phospholipids ortriacylglycerols; necessary for proper development (particularly in thedeveloping infant brain) and for tissue formation and repair; and,precursors to several biologically active eicosanoids of importance inmammals (e.g., prostacyclins, eicosanoids, leukotrienes,prostaglandins). Additionally, a high intake of long-chain ω-3 PUFAsproduces cardiovascular protective effects (Dyerberg et al., Amer. J.Clin. Nutr. 28:958-966 (1975); Dyerberg et al., Lancet. 2(8081):117-119(1978); Shimokawa, H., World Rev. Nutr. Diet 88:100-108 (2001); vonSchacky et al., World Rev. Nutr. Diet 88:90-99 (2001)). Numerous otherstudies document wide-ranging health benefits conferred byadministration of omega-3 and/or omega-6 PUFAs against a variety ofsymptoms and diseases (e.g., asthma, psoriasis, eczema, diabetes,cancer).

Today, a variety of different hosts including plants, algae, fungi andyeast are being investigated as means for commercial PUFA production vianumerous divergent efforts. Although the natural PUFA-producingabilities of the host organisms are sometimes essential to a givenmethodology, genetic engineering has also proven that the naturalabilities of some hosts (even those natively limited to LA and ALA fattyacid production) can be substantially altered to result in high-levelproduction of various long-chain omega-3/omega-6 PUFAs. Whether thiseffect is the result of natural abilities or recombinant technology,production of arachidonic acid (ARA; 20:4 ω-6), eicosapentaenoic acid(EPA; 20:5 ω-3) and docosahexaenoic acid (DHA; 22:6 ω-3) all requireexpression of either the delta-9 elongase/delta-8 desaturase pathway(which operates in some organisms, such as euglenoid species and whichis characterized by the production of eicosadienoic acid (EDA; 20:2 ω-6)and/or eicosatrienoic acid (ETrA; 20:3 ω-3)) or the delta-6desaturase/delta-6 elongase pathway (which is predominantly found inalgae, mosses, fungi, nematodes and humans and which is characterized bythe production of γ-linoleic acid (GLA; 18:3 ω-6) and/or stearidonicacid (STA; 18:4 ω-3)) (FIG. 6). A delta-6 elongase is also known as aC_(18/20) elongase.

The delta-8 desaturase enzymes identified thus far have the ability toconvert both EDA to dihomo-γ-linolenic acid (DGLA; 20:3) and ETrA toeicosatetraenoic acid (ETA; 20:4) (wherein ARA are EPA are subsequentlysynthesized from DGLA and ETA, respectively, following reaction with adelta-5 desaturase, while DHA synthesis requires subsequent expressionof an additional C_(20/22) elongase and a delta-4 desaturase).

Based on the role delta-8 desaturase enzymes play in the synthesis ofe.g., ARA, EPA and DHA, there has been effort to identify andcharacterize these enzymes. Initial efforts on the isolation andcharacterization of delta-8 desaturases from Euglena gracilis; and,several sequence variations within the Euglena gracilis delta-8desaturase have been reported (see, e.g., Wallis et al., Arch. Biochem.and Biophys. 365(2):307-316 (1999); PCT Publication No. WO 2000/34439;U.S. Pat. No. 6,825,017; PCT Publication No. WO 2004/057001). Also,Applicants'Assignee's co-pending applications having U.S. applicationSer. Nos. 11/166,003 and 11/166,993 filed Jun. 24, 2005 (Attorney DocketNos. BB-1547 and CL-3150, respectively (PCT Publication Nos. WO2006/012325 and WO 2006/012326; both published Feb. 2, 2006)) disclosesamino acid and nucleic acid sequences for a Euglena gracilis delta-8desaturase.

More recently, PCT Publication No. WO 2005/103253 (published Apr. 22,2005) discloses amino acid and nucleic acid sequences for a delta-8desaturase enzyme from Pavlova salina (see also U.S. Publication No.2005/0273885). Sayanova et al. (FEBS Lett. 580:1946-1952 (2006))describes the isolation and characterization of a cDNA from the freeliving soil amoeba Acanthamoeba castellanii that, when expressed inArabidopsis, encodes a C₂₀ delta-8 desaturase. Also, Applicants'Assignee's co-pending application having U.S. patent application Ser.No. 11/737,772 (filed Apr. 20, 2007; Attorney Docket No. BB-1566))discloses amino acid and nucleic acid sequences for a delta-8 desaturaseenzyme from Pavlova lutheri (CCMP459). U.S. patent application Ser. No.11/876,115 (filed Oct. 22, 2007; Attorney Docket No. BB-1574) disclosesamino acid and nucleic acid sequences for a delta-8 desaturase enzymefrom Tetruetreptia pornquetensis CCMP1491, Eutreptiella sp. CCMP389 andEutreptiella cf_(—) gymnastica CCMP1594.

Based on the utility of expressing delta-8 desaturases in conjunctionwith delta-9 elongases, there has also been considerable effort toidentify and characterize delta-9 elongases from various sources. Adelta-9 elongase from Isochrysis galbana has been publicly available(described in GenBank Accession No. AAL37626, as well as PCT PublicationNo. WO 02/077213). Applicants'

Assignee's co-pending application having U.S. application Ser. No.11/601,563 (filed Nov., 16, 2006, which published May 24, 2007; AttorneyDocket No. BB-1562)), discloses a delta-9 elongase from Eulgenagracilis.

Applicants' Assignee has a number of patent applications concerning theproduction of PUFAs in oleaginous yeasts (i.e., Yarrowia lipolytica),including: PCT Publication Nos. WO 2004/101757 and WO 2004/101753 (bothpublished Nov. 25, 2004); U.S. application Ser. No. 11/265,761 (filedNov. 2, 2005); U.S. application Ser. No. 11/264,784 (filed Nov. 1,2005); and U.S. application Ser. No. 11/264,737 (filed Nov. 1, 2005).

Relatedly, PCT Publication No. WO 2004/071467 (published Aug. 26, 2004;Attorney Docket No. BB-1538) concerns the production of PUFAs in plants,while PCT Publication No. WO 2004/071178 (published Aug. 26, 2004)concerns annexin promoters and their use in expression of transgenes inplants; both are Applicants' Assignee's copending applications.

SUMMARY OF THE INVENTION

The present invention concerns an isolated polynucleotide comprising:

-   -   (a) a nucleotide sequence encoding a polypeptide having delta-8        desaturase activity, wherein the polypeptide has at least 80%        amino acid identity, based on the Clustal V method of alignment,        when compared to an amino acid sequence as set forth in SEQ ID        NO:21, SEQ ID NO:22, SEQ ID NO:23 or SEQ ID NO:24;    -   (b) a nucleotide sequence encoding a polypeptide having delta-8        desaturase activity, wherein the nucleotide sequence has at        least 80% sequence identity, based on the BLASTN method of        alignment, when compared to a nucleotide sequence as set forth        in SEQ ID NO:17, SEQ ID NO:18, SEQ ID NO:19 or SEQ ID NO:20;    -   (c) a nucleotide sequence encoding a polypeptide having delta-8        desaturase activity, wherein the nucleotide sequence hybridizes        under stringent conditions to a nucleotide sequence as set forth        in SEQ ID NO:17, SEQ ID NO:18, SEQ ID NO:19 or SEQ ID NO:20; or    -   (d) a complement of the nucleotide sequence of (a), (b) or (c),        wherein the complement and the nucleotide sequence consist of        the same number of nucleotides and are 100% complementary.

In a second embodiment, the invention concerns a recombinant DNAconstruct comprising any of the isolated polynucleotides of theinvention operably linked to at least one regulatory sequence.

In a third embodiment, the invention concerns a plant cell comprising inits genome the recombinant DNA construct of the invention.

In a fourth embodiment, the invention concerns a method for transforminga plant cell, comprising transforming a plant cell with a recombinantconstruct of the invention or an isolated polynucleotide of theinvention and selecting those plant cells transformed with therecombinant construct or the isolated polynucleotide.

In a fifth embodiment, the invention concerns transgenic seed comprisingin its genome the recombinant construct of the invention or a transgenicseed obtained from a plant made by a method of the invention. Also ofinterest is oil or by-products obtained from such transgenic seeds.

In a sixth embodiment, the invention concerns a method for makinglong-chain polyunsaturated fatty acids in a plant cell comprising:

-   -   (a) transforming a plant cell with the recombinant construct of        the invention; and    -   (b) selecting those transformed plant cells that make long-chain        polyunsaturated fatty acids.

In a seventh embodiment, the invention concerns a method for producingat least one polyunsaturated fatty acid in an oilseed plant cellcomprising:

-   -   (a) transforming an oilseed plant cell with a first recombinant        DNA construct comprising an isolated polynucleotide encoding at        least one delta-8 desaturase polypeptide, operably linked to at        least one regulatory sequence and at least one additional        recombinant DNA construct comprising an isolated polynucleotide,        operably linked to at least one regulatory sequence, encoding a        polypeptide selected from the group consisting of a delta-4        desaturase, a delta-5 desaturase, a delta-6 desaturase, a        delta-8 desaturase, a delta-12 desaturase, a delta-15        desaturase, a delta-17 desaturase, a delta-9 desaturase, a        delta-9 elongase, a C_(14/16) elongase, a C_(16/18) elongase, a        C_(18/20) elongase and a C_(20/22) elongase;    -   (b) regenerating an oilseed plant from the transformed cell of        step (a); and    -   (c) selecting those seeds obtained from the plants of step (b)        having an altered level of polyunsaturated fatty acids when        compared to the level in seeds obtained from a nontransformed        oilseed plant.

In an eighth embodiment, the invention concerns an oilseed plantcomprising in its genome the recombinant construct of the invention.Suitable oilseed plants include, but are not limited to, soybean,Brassica species, sunflower, maize, cotton, flax and safflower.

In a ninth embodiment, the invention concerns an oilseed plantcomprising:

-   -   (a) a first recombinant DNA construct comprising an isolated        polynucleotide encoding at least one delta-8 desaturase        polypeptide, operably linked to at least one regulatory        sequence; and    -   (b) at least one additional recombinant DNA construct comprising        an isolated polynucleotide, operably linked to at least one        regulatory sequence, encoding a polypeptide selected from the        group consisting of a delta-4 desaturase, a delta-5 desaturase,        a delta-6 desaturase, a delta-8 desaturase, a delta-12        desaturase, a delta-15 desaturase, a delta-17 desaturase, a        delta-9 desaturase, a delta-9 elongase, a C_(14/16) elongase, a        C_(16/18) elongase, a C_(18/20) elongase and a C_(20/22)        elongase.

Also of interest are transgenic seeds obtained from such oilseed plantsas well as oil or by-products obtained from these transgenic seeds. Apreferred product is lecithin.

In a tenth embodiment, the invention concerns food or feed incorporatingan oil or seed of the invention or food or feed comprising an ingredientderived from the processing of the seeds.

In an eleventh embodiment, the invention concerns a method for makinglong-chain polyunsaturated fatty acids in a plant cell having a reducedlevel of by-product fatty acids, said method comprising:

-   -   (a) transforming a plant host cell with at least one recombinant        DNA construct comprising an isolated polynucleotide encoding at        least two delta-8 desaturases operably linked to at least one        regulatory sequence; and    -   (b) selecting those transformed plant host cells obtained having        a reduced level of by-product fatty acids, when compared to the        level of such metabolic by-product fatty acids in a transformed        host cell having at least one recombinant DNA construct        comprising an isolated polynucleotide encoding one delta-8        desaturase operably linked to a regulatory sequence.

In a twelfth embodiment, the invention concerns progeny plants obtainedfrom obtained from a plant made by the method of the invention or anoilseed plant of the invention.

Biological Deposits

The following plasmid has been deposited with the American Type Culture

Collection (ATCC), 10801 University Boulevard, Manassas, Va. 20110-2209,and bears the following designation, Accession Number and date ofdeposit (Table 1).

TABLE 1 ATCC Deposit Plasmid Accession Number Date of Deposit pKR72PTA-6019 May 28, 2004

BRIEF DESCRIPTION OF THE DRAWINGS AND SEQUENCE LISTINGS

The invention can be more fully understood from the following detaileddescription and the accompanying drawings and Sequence Listing, whichform a part of this application.

FIG. 1 is a representative omega-3 and omega-6 fatty acid pathwayproviding for the conversion of myristic acid through variousintermediates to DHA.

FIG. 2 is a map of plasmid pY115 (SEQ ID NO:34).

FIG. 3A is a map of plasmid pY175 (SEQ ID NO:35).

FIG. 3B is a map of plasmid pY176 (SEQ ID NO:36).

FIG. 3C is a map of plasmid pY177 (SEQ ID NO:37).

FIG. 3D is a map of plasmid and pY178 (SEQ ID NO:38).

FIG. 4 are the fatty acid profiles for Yarrowia lipolytica expressingpY175-pY178 (see Example 4).

FIG. 5 is a map of pKR1152 (SEQ ID NO:47).

FIG. 6 shows a chromatogram of the lipid profile of an Euglena anabaenacell extract as described in the Examples.

FIGS. 7A, 7B and 7C show a Clustal V alignment of the delta-8 desaturasesequences for EaD8Des1 (SEQ ID NO:21), EaD8Des2 (SEQ ID NO:22), EaD8Des3(SEQ ID NO:23) and EaD8Des4 (SEQ ID NO:24), and the corrected Euglenagracilis delta-8 desaturase amino acid sequence (EgD8; SEQ ID NO:25;described as Eg5 in PCT Application No. WO 2006/012325).

FIG. 8 is a chart setting forth a comparison of the percent identity(and percent divergence in the lower half triangle), among the fivedelta-8 desaturase sequences aligned in FIGS. 7A, 7B and 7C.

FIGS. 9A and 9B shows a comparison of the nucleotide sequences ofEaD8Des3 (SEQ ID NO:19) and EaD8S (SEQ ID NO:48).

FIG. 10 is a map of plasmid pEaD8S (SEQ ID NO:49).

FIG. 11 is a map of plasmid pKR1150 (SEQ ID NO:60).

FIG. 12 is a map of plasmid pKR1192 (SEQ ID NO:66).

FIG. 13 shows the average fatty acid profiles (average of 5 soybeansomatic embryos) for 5 events transformed with pKR1152 having thehighest average DGLA. Fatty acids are identified as 16:0 (palmitate),18:0 (stearic acid), 18:1 (oleic acid), LA, ALA, EDA, ERA, DGLA and ETA.Fatty acid compositions are expressed as a weight percent (wt. %) oftotal fatty acids. Elongation activity is expressed as delta-9elongation of C18 fatty acids (C18% delta-9 elong), calculated accordingto the following formula: ([product]/[substrate+product])*100. Morespecifically, the combined percent elongation for LA and ALA isdetermined as: ([DGLA+ETA+EDA+ERA]/[LA+ALA+DGLA+ETA+EDA+ERA])*100. Tthecombined percent desaturation for EDA and ERA is shown as “C20% delta-8desat”, determined as: ([DGLA+ETA]/[DGLA+ETA+EDA+ERA])*100. This is alsoreferred to as the overall % desaturation.

FIG. 14 shows the average fatty acid profiles (average of 5 soybeansomatic embryos) for 5 events transformed with pKR1150 having thehighest average DGLA. Fatty acids are identified as 16:0 (palmitate),18:0 (stearic acid), 18:1 (oleic acid), LA, ALA, EDA, ERA, DGLA and ETA.Fatty acid compositions are expressed as a weight percent (wt. %) oftotal fatty acids. Elongation activity is expressed as delta-9elongation of C18 fatty acids (C18% delta-9 elong), calculated accordingto the following formula: ([product]/[substrate+product])*100. Morespecifically, the combined percent elongation for LA and ALA isdetermined as: ([DGLA+ETA+EDA+ERA]/[LA+ALA+DGLA+ETA+EDA+ERA])*100. Tthecombined percent desaturation for EDA and ERA is shown as “020% delta-8desat”, determined as: ([DGLA+ETA]/[DGLA+ETA+EDA+ERA])*100. This is alsoreferred to as the overall % desaturation.

FIG. 15 shows the lipid profiles of T2 bulk Arabidopsis seed for the 21transformed events. Fatty acids are identified as 16:0 (palmitate), 18:0(stearic acid), 18:1 (oleic acid), LA, ALA, 20:0 (eicosanoic acid), 20:1(eicosenoic acid), EDA, DGLA, ERA and ETA; and, fatty acids areexpressed as a weight percent (wt. %) of total fatty acids. The combinedpercent desaturation for EDA and ERA is shown as “020% delta-8 desat”,determined as: ([DGLA+ETA]/[DGLA+ETA+EDA+ERA])*100. This is alsoreferred to as the overall % desaturation.

The sequence descriptions summarize the Sequences Listing attachedhereto. The Sequence Listing contains one letter codes for nucleotidesequence characters and the single and three letter codes for aminoacids as defined in the IUPAC-IUB standards described in Nucleic AcidsResearch 13:3021-3030 (1985) and in the Biochemical Journal219(2):345-373 (1984).

SEQ ID NO:1 is the nucleotide sequence of the Euglena anabaena delta-8desaturase partial sequence.

SEQ ID NO:2 is the amino acid sequence of the Euglena gracilis delta-8desaturase CDS (Eg5).

SEQ ID NO:3 is the nucleotide sequence of the vector-specific primerpDonor222Eg5-1.

SEQ ID NO:4 is the nucleotide sequence of D8DEG3-1. SEQ ID NO:5 is thenucleotide sequence of D8DEG3-2.

SEQ ID NO:6 is the nucleotide sequence of D8DEG3-3.

SEQ ID NO:7 is the nucleotide sequence of D8DEG3-4.

SEQ ID NO:8 is the nucleotide sequence of the T7 primer. SEQ ID NO:9 isthe nucleotide sequence of M13-28Rev.

SEQ ID NO:10 is the nucleotide sequence of pHD23-1.

SEQ ID NO:11 is the amino acid sequence of Euglena gracilis delta-8desaturase (NCBI Accession No. AAD45877).

SEQ ID NO:12 is the nucleotide sequence of EaD8seq-1.

SEQ ID NO:13 is the nucleotide sequence of pLF118-1.

SEQ ID NO:14 is the nucleotide sequence of pLF118-2.

SEQ ID NO:15 is the nucleotide sequence of pLF118-3.

SEQ ID NO:16 is the nucleotide sequence of pLF118-4.

SEQ ID NO:17 is the coding sequence of the Euglena anabaena delta-8desaturase (EaD8Des1 CDS).

SEQ ID NO:18 is the coding sequence of the Euglena anabaena delta-8desaturase (EaD8Des2 CDS).

SEQ ID NO:19 is the coding sequence of the Euglena anabaena delta-8desaturase (EaD8Des3 CDS).

SEQ ID NO:20 is the coding sequence of the Euglena anabaena delta-8desaturase (EaD8Des4 CDS).

SEQ ID NO:21 is the amino acid sequence of the Euglena anabaena delta-8desaturase (EaD8Des1).

SEQ ID NO:22 is the amino acid sequence of the Euglena anabaena delta-8desaturase (EaD8Des2).

SEQ ID NO:23 is the amino acid sequence of the Euglena anabaena delta-8desaturase (EaD8Des3).

SEQ ID NO:24 is the amino acid sequence of the Euglena anabaena delta-8desaturase (EaD8Des4).

SEQ ID NO:25 is the amino acid sequence of the corrected Euglenagracilis delta-8 desaturase (EgD8).

SEQ ID NO:26 is the nucleotide sequence of oligonucleotide EaD8-5. SEQID NO:27 is the nucleotide sequence of oligonucleotide EaD8-3.

SEQ ID NO:28 is the nucleotide sequence of pLF120-1.

SEQ ID NO:29 is the nucleotide sequence of pLF120-2.

SEQ ID NO:30 is the nucleotide sequence of pLF120-3.

SEQ ID NO:31 is the nucleotide sequence of pLF120-4.

SEQ ID NO:32 is the nucleotide sequence of pDMW263.

SEQ ID NO:33 is the nucleotide sequence of pDMW237.

SEQ ID NO:34 is the nucleotide sequence of pY115.

SEQ ID NO:35 is the nucleotide sequence of pY175.

SEQ ID NO:36 is the nucleotide sequence of pY176.

SEQ ID NO:37 is the nucleotide sequence of pY177.

SEQ ID NO:38 is the nucleotide sequence of pY178.

SEQ ID NO:39 is the coding sequence of the Euglena gracilis delta-9elongase.

SEQ ID NO:40 is the nucleotide sequence of the Euglena gracilis elongasesense oligonucleotide oEugEL1-1.

SEQ ID NO:41 is the nucleotide sequence of the Euglena gracilis senseoligonucleotide oEugEL1-2.

SEQ ID NO:42 is the nucleotide sequence of pKR906.

SEQ ID NO:43 is the nucleotide sequence of pKR72.

SEQ ID NO:44 is the nucleotide sequence of pKR912.

SEQ ID NO:45 is the nucleotide sequence of pKR457.

SEQ ID NO:46 is the nucleotide sequence of pKR1138.

SEQ ID NO:47 is the nucleotide sequence of pKR1152.

SEQ ID NO:48 is the nucleotide sequence of the codon optimized EaD8Sgene.

SEQ ID NO:49 is the nucleotide sequence of plasmid pEaD8S.

SEQ ID NO:50 is the nucleotide sequence of pLF121-1.

SEQ ID NO:51 is the nucleotide sequence of pLF121-2.

SEQ ID NO:52 is the coding sequence of the Euglena anabaena delta-9elongase-1 (EaD9Elo1).

SEQ ID NO:53 is the coding sequence of the Euglena anabaena delta-9elongase-2 (EaD9Elo2).

SEQ ID NO:54 is the amino acid sequence of the Euglena anabaena delta-9elongase-1 (EaD9Elo1).

SEQ ID NO:55 is the amino acid sequence of the Euglena anabaena delta-9elongase-2 (EaD9Elo2).

SEQ ID NO:56 is the nucleotide sequence of oligonucleotide oEAd9el1-1.

SEQ ID NO:57 is the nucleotide sequence of oligonucleotide oEAd9el1-2.

SEQ ID NO:58 is the nucleotide sequence of pKR1137.

SEQ ID NO:59 is the nucleotide sequence of pKR1140.

SEQ ID NO:60 is the nucleotide sequence of pKR1150.

SEQ ID NO:61 is the nucleotide sequence of pKR1173.

SEQ ID NO:62 is the nucleotide sequence of pKR393.

SEQ ID NO:63 is the nucleotide sequence of pKR407.

SEQ ID NO:64 is the nucleotide sequence of pKR1176.

SEQ ID NO:65 is the nucleotide sequence of pKR1178.

SEQ ID NO:66 is the nucleotide sequence of pKR1192.

DETAILED DESCRIPTION OF THE INVENTION

The disclosure of each reference set forth herein is hereby incorporatedby reference in its entirety.

As used herein and in the appended claims, the singular forms “a”, “an”,and “the” include plural reference unless the context clearly dictatesotherwise. Thus, for example, reference to “a plant” includes aplurality of such plants, reference to “a cell” includes one or morecells and equivalents thereof known to those skilled in the art, and soforth.

The present invention relates to delta-8 desaturase enzymes and nucleicacid for encoding the same isolated from Euglena anabaena. These areuseful for, inter alia, for the manipulation of biochemical pathways forthe production of healthful PUFAs. Thus, the subject invention findsmany applications. PUFAs, or derivatives thereof, made by themethodology disclosed herein can be used as dietary substitutes, orsupplements, particularly infant formulas, for patients undergoingintravenous feeding or for preventing or treating malnutrition.Alternatively, the purified PUFAs (or derivatives thereof) may beincorporated into cooking oils, fats or margarines formulated so that innormal use the recipient would receive the desired amount for dietarysupplementation. The PUFAs may also be incorporated into infantformulas, nutritional supplements or other food products and may finduse as anti-inflammatory or cholesterol lowering agents. Optionally, thecompositions may be used for pharmaceutical use (human or veterinary).In this case, the PUFAs are generally administered orally but can beadministered by any route by which they may be successfully absorbed,e.g., parenterally (e.g., subcutaneously, intramuscularly orintravenously), rectally, vaginally or topically (e.g., as a skinointment or lotion).

Supplementation of humans or animals with PUFAs produced by recombinantmeans can result in increased levels of the added PUFAs, as well astheir metabolic progeny. For example, treatment with EPA can result notonly in increased levels of EPA, but also downstream products of EPAsuch as eicosanoids (i.e., prostaglandins, leukotrienes, thromboxanes).Complex regulatory mechanisms can make it desirable to combine variousPUFAs, or add different conjugates of PUFAs, in order to prevent,control or overcome such mechanisms to achieve the desired levels ofspecific PUFAs in an individual.

In the context of this disclosure, a number of terms and abbreviationsare used. The following definitions are provided.

“Open reading frame” is abbreviated ORF.

“Polymerase chain reaction” is abbreviated PCR.

“American Type Culture Collection” is abbreviated ATCC.

“Polyunsaturated fatty acid(s)” is abbreviated PUFA(s).

“Triacylglycerols” are abbreviated TAGs.

The term “fatty acids” refers to long-chain aliphatic acids (alkanoicacids) of varying chain lengths, from about C₁₂ to C₂₂ (although bothlonger and shorter chain-length acids are known). The predominant chainlengths are between C₁₆ and C₂₂. Additional details concerning thedifferentiation between “saturated fatty acids” versus “unsaturatedfatty acids”, “monounsaturated fatty acids” versus “polyunsaturatedfatty acids” (or “PUFAs”), and “omega-6 fatty acids” (ω-6 or n-6) versus“omega-3 fatty acids” (ω-3 or n-3) are provided in PCT Publication No.WO 2004/101757.

Fatty acids are described herein by a simple notation system of “X:Y”,wherein X is number of carbon (C) atoms in the particular fatty acid andY is the number of double bonds. The number following the fatty aciddesignation indicates the position of the double bond from the carboxylend of the fatty acid with the “c” affix for the cis-configuration ofthe double bond (e.g., palmitic acid (16:0), stearic acid (18:0), oleicacid (18:1, 9c), petroselinic acid (18:1, 6c), LA (18:2, 9c,12c), GLA(18:3, 6c,9c,12c) and ALA (18:3, 9c,12c,15c)). Unless otherwisespecified, 18:1, 18:2 and 18:3 refer to oleic, LA and ALA fatty acids,respectively. If not specifically written as otherwise, double bonds areassumed to be of the cis configuration. For instance, the double bondsin 18:2 (9,12) would be assumed to be in the cis configuration.

Nomenclature used to describe PUFAs in the present disclosure is shownbelow in Table 2. In the column titled “Shorthand Notation”, theomega-reference system is used to indicate the number of carbons, thenumber of double bonds and the position of the double bond closest tothe omega carbon, counting from the omega carbon (which is numbered 1for this purpose). The remainder of the table summarizes the commonnames of omega-3 and omega-6 fatty acids and their precursors, theabbreviations that will be used throughout the remainder of thespecification, and each compounds' chemical name.

TABLE 2 Nomenclature of Polyunsaturated Fatty Acids and PrecursorsCommon Shorthand Name Abbreviation Chemical Name Notation myristic —tetradecanoic 14:0 palmitic PA hexadecanoic 16:0 palmitoleic —9-hexadecenoic 16:1 stearic — octadecanoic 18:0 oleic —cis-9-octadecenoic 18:1 linoleic LA cis-9,12-octadecadienoic 18:2 ω-6gamma- GLA cis-6,9,12- 18:3 ω-6 linolenic octadecatrienoic eicosadienoicEDA cis-11,14-eicosadienoic 20:2 ω-6 dihomo- DGLAcis-8,11,14-eicosatrienoic 20:3 ω-6 gamma- linolenic sciadonic SCIcis-5,11,14-eicosatrienoic 20:3b ω-6 arachidonic ARA cis-5,8,11,14- 20:4ω-6 eicosatetraenoic alpha-linolenic ALA cis-9,12,15- 18:3 ω-3octadecatrienoic stearidonic STA cis-6,9,12,15- 18:4 ω-3octadecatetraenoic eicosatrienoic ETrA or ERA cis-11,14,17- 20:3 ω-3eicosatrienoic eicosatetraenoic ETA cis-8,11,14,17- 20:4 ω-3eicosatetraenoic juniperonic JUP cis-5,11,14,17- 20:4b ω-3eicosatrienoic eicosapentaenoic EPA cis-5,8,11,14,17- 20:5 ω-3eicosapentaenoic docosapentaenoic DPA cis-7,10,13,16,19- 22:5 ω-3docosapentaenoic docosahexaenoic DHA cis-4,7,10,13,16,19- 22:6 ω-3docosahexaenoic

A metabolic pathway, or biosynthetic pathway, in a biochemical sense,can be regarded as a series of chemical reactions occurring within acell, catalyzed by enzymes, to achieve either the formation of ametabolic product to be used or stored by the cell, or the initiation ofanother metabolic pathway (then called a flux generating step). Many ofthese pathways are elaborate, and involve a step by step modification ofthe initial substance to shape it into a product having the exactchemical structure desired.

The term “PUFA biosynthetic pathway” refers to a metabolic process thatconverts oleic acid to LA, EDA, GLA, DGLA, ARA, ALA, STA, ETrA, ETA,EPA, DPA and DHA. This process is well described in the literature(e.g., see PCT Publication No. WO 2006/052870). Simplistically, thisprocess involves elongation of the carbon chain through the addition ofcarbon atoms and desaturation of the molecule through the addition ofdouble bonds, via a series of special desaturation and elongationenzymes (i.e., “PUFA biosynthetic pathway enzymes”) present in theendoplasmic reticulim membrane. More specifically, “PUFA biosyntheticpathway enzyme” refers to any of the following enzymes (and genes whichencode said enzymes) associated with the biosynthesis of a PUFA,including: a delta-4 desaturase, a delta-5 desaturase, a delta-6desaturase, a delta-12 desaturase, a delta-15 desaturase, a delta-17desaturase, a delta-9 desaturase, a delta-8 desaturase, a delta-9elongase, a C_(14/16) elongase, a C_(16/18) elongase, a C_(18/20)elongase and/or a C_(20/22) elongase.

The term “omega-3/omega-6 fatty acid biosynthetic pathway” refers to aset of genes which, when expressed under the appropriate conditionsencode enzymes that catalyze the production of either or both omega-3and omega-6 fatty acids. Typically the genes involved in theomega-3/omega-6 fatty acid biosynthetic pathway encode PUFA biosyntheticpathway enzymes. A representative pathway is illustrated in FIG. 1,providing for the conversion of myristic acid through variousintermediates to DHA, which demonstrates how both omega-3 and omega-6fatty acids may be produced from a common source. The pathway isnaturally divided into two portions where one portion will generateomega-3 fatty acids and the other portion, omega-6 fatty acids.

The term “functional” as used herein in context with the omega-3/omega-6fatty acid biosynthetic pathway means that some (or all of) the genes inthe pathway express active enzymes, resulting in in vivo catalysis orsubstrate conversion. It should be understood that “omega-3/omega-6fatty acid biosynthetic pathway” or “functional omega-3/omega-6 fattyacid biosynthetic pathway” does not imply that all the PUFA biosyntheticpathway enzyme genes are required, as a number of fatty acid productswill only require the expression of a subset of the genes of thispathway.

The term “delta-9 elongase/delta-8 desaturase pathway” refers to abiosynthetic pathway for production of long-chain PUFAs. This pathway,at a minimum, comprises a delta-9 elongase and a delta-8 desaturase,thereby enabling biosynthesis of DGLA and/or ETA from LA and ALA,respectively. With expression of other desaturases and elongases, ARA,EPA, DPA and DHA may also be synthesized. This pathway may beadvantageous in some embodiments, as the biosynthesis of GLA and/or STAis excluded.

The term “intermediate fatty acid” refers to any fatty acid produced ina fatty acid metabolic pathway that can be further converted to anintended product fatty acid in this pathway by the action of othermetabolic pathway enzymes. For instance, when EPA is produced using thedelta-9 elongase/delta-8 desaturase pathway, EDA, ETrA, DGLA, ETA andARA can be produced and are considered “intermediate fatty acids” sincethese fatty acids can be further converted to EPA via action of othermetabolic pathway enzymes.

The term “by-product fatty acid” refers to any fatty acid produced in afatty acid metabolic pathway that is not the intended fatty acid productof the pathway nor an “intermediate fatty acid” of the pathway. Forinstance, when EPA is produced using the delta-9 elongase/delta-8desaturase pathway, sciadonic acid (SCl) and juniperonic acid (JUP) alsocan be produced by the action of a delta-5 desaturase on either EDA orETrA, respectively. They are considered to be “by-product fatty acids”since neither can be further converted to EPA by the action of othermetabolic pathway enzymes.

The terms “triacylglycerol”, “oil” and “TAGs” refer to neutral lipidscomposed of three fatty acyl residues esterified to a glycerol molecule(and such terms will be used interchangeably throughout the presentdisclosure herein). Such oils can contain long-chain PUFAs, as well asshorter saturated and unsaturated fatty acids and longer chain saturatedfatty acids. Thus, “oil biosynthesis” generically refers to thesynthesis of TAGs in the cell.

“Percent (%) PUFAs in the total lipid and oil fractions” refers to thepercent of PUFAs relative to the total fatty acids in those fractions.The term “total lipid fraction” or “lipid fraction” both refer to thesum of all lipids (i.e., neutral and polar) within an oleaginousorganism, thus including those lipids that are located in thephosphatidylcholine (PC) fraction, phosphatidyletanolamine (PE) fractionand triacylglycerol (TAG or oil) fraction. However, the terms “lipid”and “oil” will be used interchangeably throughout the specification.

The terms “conversion efficiency” and “percent substrate conversion”refer to the efficiency by which a particular enzyme (e.g., adesaturase) can convert substrate to product. The conversion efficiencyis measured according to the following formula:([product]/[substrate+product])*100, where ‘product’ includes theimmediate product and all products in the pathway derived from it.

“Desaturase” is a polypeptide that can desaturate, i.e., introduce adouble bond, in one or more fatty acids to produce a fatty acid orprecursor of interest. Despite use of the omega-reference systemthroughout the specification to refer to specific fatty acids, it ismore convenient to indicate the activity of a desaturase by countingfrom the carboxyl end of the substrate using the delta-system. Ofparticular interest herein are delta-8 desaturases that will desaturatea fatty acid between the eighth and ninth carbon atom numbered from thecarboxyl-terminal end of the molecule and that can, for example,catalyze the conversion of EDA to DGLA and/or ETrA to ETA. Other usefulfatty acid desaturases include, for example: (1) delta-5 desaturasesthat catalyze the conversion of DGLA to ARA and/or ETA to EPA; (2)delta-6 desaturases that catalyze the conversion of LA to GLA and/or ALAto STA; (3) delta-4 desaturases that catalyze the conversion of DPA toDHA; (4) delta-12 desaturases that catalyze the conversion of oleic acidto LA; (5) delta-15 desaturases that catalyze the conversion of LA toALA and/or GLA to STA; (6) delta-17 desaturases that catalyze theconversion of ARA to EPA and/or DGLA to ETA; and (7) delta-9 desaturasesthat catalyze the conversion of palmitic acid to palmitoleic acid (16:1)and/or stearic acid to oleic acid (18:1). In the art, delta-15 anddelta-17 desaturases are also occasionally referred to as “omega-3desaturases”, “ω-3 desaturases”, and/or “ω-3 desaturases”, based ontheir ability to convert omega-6 fatty acids into their omega-3counterparts (e.g., conversion of LA into ALA and ARA into EPA,respectively). In some embodiments, it is most desirable to empiricallydetermine the specificity of a particular fatty acid desaturase bytransforming a suitable host with the gene for the fatty acid desaturaseand determining its effect on the fatty acid profile of the host.

For the purposes herein, the term “EaD8Des1” refers to a delta-8desaturase enzyme (SEQ ID NO:21) isolated from Euglena anabaena, encodedby SEQ ID NO:17 herein. The term “EaD8Des2” refers to a delta-8desaturase enzyme (SEQ ID NO:22) isolated from Euglena anabaena, encodedby SEQ ID NO:18 herein.

Likewise, the term “EaD8Des3” refers to a delta-8 desaturase enzyme (SEQID NO:23) isolated from Euglena anabaena, encoded by SEQ ID NO:19herein. The term “EaD8Des4” refers to a delta-8 desaturase enzyme (SEQID NO:24) isolated from Euglena anabaena, encoded by SEQ ID NO:20herein.

Similarly, the term “EgD8” refers to a delta-8 desaturase enzyme (SEQ IDNO:2 is the nucleic acid coding sequence) isolated from Euglenagracilis. EgD8 is 100% identical and functionally equivalent to “Eg5”,as described in PCT Publication Nos. WO 2006/012325 and WO 2006/012326(SEQ ID NO:2 of U.S. Publication No. 20050287652-A1).

The term “elongase system” refers to a suite of four enzymes that areresponsible for elongation of a fatty acid carbon chain to produce afatty acid that is two carbons longer than the fatty acid substrate thatthe elongase system acts upon.

More specifically, the process of elongation occurs in association withfatty acid synthase, whereby CoA is the acyl carrier (Lassner et al.,Plant Cell 8:281-292 (1996)). In the first step, which has been found tobe both substrate-specific and also rate-limiting, malonyl-CoA iscondensed with a long-chain acyl-CoA to yield carbon dioxide (CO₂) and aβ-ketoacyl-CoA (where the acyl moiety has been elongated by two carbonatoms). Subsequent reactions include reduction to β-hydroxyacyl-CoA,dehydration to an enoyl-CoA and a second reduction to yield theelongated acyl-CoA. Examples of reactions catalyzed by elongase systemsare the conversion of GLA to DGLA, STA to ETA, LA to EDA, ALA to ETRAand EPA to DPA.

For the purposes herein, an enzyme catalyzing the first condensationreaction (i.e., conversion of malonyl-CoA and long-chain acyl-CvoA toJ3-ketoacyl-CoA) will be referred to generically as an “elongase”. Ingeneral, the substrate selectivity of elongases is somewhat broad butsegregated by both chain length and the degree of unsaturation.Accordingly, elongases can have different specificities. For example, aC_(14/16) elongase will utilize a C₁₄ substrate (e.g., myristic acid), aC_(16/18) elongase will utilize a C₁₆ substrate (e.g., palmitate), aC_(18/20) elongase will utilize a C₁₈ substrate (e.g., GLA, STA) and aC_(20/22) elongase will utilize a C₂₀ substrate (e.g., EPA). Similarily,a “delta-9 elongase” may be able to catalyze the conversion of LA to EDAand/or ALA to ETrA. It is important to note that some elongases havebroad specificity and thus a single enzyme may be capable of catalyzingseveral elongase reactions. Thus, for example, a delta-9 elongase mayalso act as a C_(16/18) elongase, C_(18/20) elongase and/or C_(20/22)elongase and may have alternate, but not preferred, specificities fordelta-5 and delta-6 fatty acids such as EPA and/or GLA, respectively.

For the purposes herein, the term “IgD9e” refers to a delta-9 elongase(NCBI Accession No. AAL37626 [GI 17226123], locus AAL37626, CDSAF390174; GenBank Accession No. AF390174) isolated from Isochrysisgalbana. In contrast, the term “IgD9eS” refers to a synthetic(codon-optimized) delta-9 elongase derived from the DNA sequence of theIsochrysis galbana delta-9 elongase which can be used for expression inYarrowia lipolytica.

Similarly for the purposes herein, the term “EgD9e” refers to a delta-9elongase isolated from Euglena gracilis, encoded by SEQ ID NO:39 (seeExample 5 herein).

As used herein, “nucleic acid” means a polynucleotide and includessingle or double-stranded polymer of deoxyribonucleotide orribonucleotide bases. Nucleic acids may also include fragments andmodified nucleotides. Thus, the terms “polynucleotide”, “nucleic acidsequence”, “nucleotide sequence” or “nucleic acid fragment” are usedinterchangeably and is a polymer of RNA or DNA that is single- ordouble-stranded, optionally containing synthetic, non-natural or alterednucleotide bases. Nucleotides (usually found in their 5′-monophosphateform) are referred to by their single letter designation as follows: “A”for adenylate or deoxyadenylate (for RNA or DNA, respectively), “C” forcytidylate or deosycytidylate, “G” for guanylate or deoxyguanylate, “U”for uridlate, “T” for deosythymidylate, “R” for purines (A or G), “Y”for pyrimidiens (C or T), “K” for G or T, “H” for A or C or T, “I” forinosine, and “N” for any nucleotide.

The terms “subfragment that is functionally equivalent” and“functionally equivalent subfragment” are used interchangeably herein.These terms refer to a portion or subsequence of an isolated nucleicacid fragment in which the ability to alter gene expression or produce acertain phenotype is retained whether or not the fragment or subfragmentencodes an active enzyme. For example, the fragment or subfragment canbe used in the design of chimeric genes to produce the desired phenotypein a transformed plant. Chimeric genes can be designed for use insuppression by linking a nucleic acid fragment or subfragment thereof,whether or not it encodes an active enzyme, in the sense or antisenseorientation relative to a plant promoter sequence.

The term “conserved domain” or “motif” means a set of amino acidsconserved at specific positions along an aligned sequence ofevolutionarily related proteins. While amino acids at other positionscan vary between homologous proteins, amino acids that are highlyconserved at specific positions indicate amino acids that are essentialin the structure, the stability, or the activity of a protein. Becausethey are identified by their high degree of conservation in alignedsequences of a family of protein homologues, they can be used asidentifiers, or “signatures”, to determine if a protein with a newlydetermined sequence belongs to a previously identified protein family.

The terms “homology”, “homologous”, “substantially similar” and“corresponding substantially” are used interchangeably herein. Theyrefer to nucleic acid fragments wherein changes in one or morenucleotide bases do not affect the ability of the nucleic acid fragmentto mediate gene expression or produce a certain phenotype. These termsalso refer to modifications of the nucleic acid fragments of the instantinvention such as deletion or insertion of one or more nucleotides thatdo not substantially alter the functional properties of the resultingnucleic acid fragment relative to the initial, unmodified fragment. Itis therefore understood, as those skilled in the art will appreciate,that the invention encompasses more than the specific exemplarysequences.

Moreover, the skilled artisan recognizes that substantially similarnucleic acid sequences encompassed by this invention are also defined bytheir ability to hybridize (under moderately stringent conditions, e.g.,0.5×SSC, 0.1% SDS, 60° C.) with the sequences exemplified herein, or toany portion of the nucleotide sequences disclosed herein and which arefunctionally equivalent to any of the nucleic acid sequences disclosedherein. Stringency conditions can be adjusted to screen for moderatelysimilar fragments, such as homologous sequences from distantly relatedorganisms, to highly similar fragments, such as genes that duplicatefunctional enzymes from closely related organisms. Post-hybridizationwashes determine stringency conditions.

The term “selectively hybridizes” includes reference to hybridization,under stringent hybridization conditions, of a nucleic acid sequence toa specified nucleic acid target sequence to a detectably greater degree(e.g., at least 2-fold over background) than its hybridization tonon-target nucleic acid sequences and to the substantial exclusion ofnon-target nucleic acids. Selectively hybridizing sequences typicallyhave about at least 80% sequence identity, or 90% sequence identity, upto and including 100% sequence identity (i.e., fully complementary) witheach other.

The term “stringent conditions” or “stringent hybridization conditions”includes reference to conditions under which a probe will selectivelyhybridize to its target sequence. Stringent conditions aresequence-dependent and will be different in different circumstances. Bycontrolling the stringency of the hybridization and/or washingconditions, target sequences can be identified which are 100%complementary to the probe (homologous probing). Alternatively,stringency conditions can be adjusted to allow some mismatching insequences so that lower degrees of similarity are detected (heterologousprobing). Generally, a probe is less than about 1000 nucleotides inlength, optionally less than 500 nucleotides in length.

Typically, stringent conditions will be those in which the saltconcentration is less than about 1.5 M Na ion, typically about 0.01 to1.0 M Na ion concentration (or other salts) at pH 7.0 to 8.3 and thetemperature is at least about 30° C. for short probes (e.g., 10 to 50nucleotides) and at least about 60° C. for long probes (e.g., greaterthan 50 nucleotides). Stringent conditions may also be achieved with theaddition of destabilizing agents such as formamide. Exemplary lowstringency conditions include hybridization with a buffer solution of 30to 35% formamide, 1 M NaCl, 1% SDS (sodium dodecyl sulphate) at 37° C.,and a wash in 1× to 2×SSC (20×SSC=3.0 M NaCl/0.3 M trisodium citrate) at50 to 55° C. Exemplary moderate stringency conditions includehybridization in 40 to 45% formamide, 1 M NaCl, 1% SDS at 37° C., and awash in 0.5× to 1×SSC at 55 to 60° C. Exemplary high stringencyconditions include hybridization in 50% formamide, 1 M NaCl, 1% SDS at37° C., and a wash in 0.1×SSC at 60 to 65° C.

Specificity is typically the function of post-hybridization washes, thecritical factors being the ionic strength and temperature of the finalwash solution. For DNA-DNA hybrids, the T_(m) can be approximated fromthe equation of Meinkoth et al., Anal. Biochem. 138:267-284 (1984):T_(m)=81.5° C.+16.6 (log M)+0.41 (% GC)−0.61 (% form)−500/L; where M isthe molarity of monovalent cations, % GC is the percentage of guanosineand cytosine nucleotides in the DNA, % form is the percentage offormamide in the hybridization solution, and L is the length of thehybrid in base pairs. The T_(m) is the temperature (under defined ionicstrength and pH) at which 50% of a complementary target sequencehybridizes to a perfectly matched probe. T_(m) is reduced by about 1° C.for each 1% of mismatching; thus, T_(m), hybridization and/or washconditions can be adjusted to hybridize to sequences of the desiredidentity. For example, if sequences with >90% identity are sought, theT_(m) can be decreased 10° C. Generally, stringent conditions areselected to be about 5° C. lower than the thermal melting point (T_(m))for the specific sequence and its complement at a defined ionic strengthand pH. However, severely stringent conditions can utilize ahybridization and/or wash at 1, 2, 3, or 4° C. lower than the thermalmelting point (T_(m)); moderately stringent conditions can utilize ahybridization and/or wash at 6, 7, 8, 9, or 10° C. lower than thethermal melting point (T_(m)); low stringency conditions can utilize ahybridization and/or wash at 11, 12, 13, 14, 15, or 20° C. lower thanthe thermal melting point (T_(m)). Using the equation, hybridization andwash compositions, and desired T_(m), those of ordinary skill willunderstand that variations in the stringency of hybridization and/orwash solutions are inherently described. If the desired degree ofmismatching results in a T_(m) of less than 45° C. (aqueous solution) or32° C. (formamide solution) it is preferred to increase the SSCconcentration so that a higher temperature can be used. An extensiveguide to the hybridization of nucleic acids is found in Tijssen,Laboratory Techniques in Biochemistry and MolecularBiology—Hybridization with Nucleic Acid Probes, Part I, Chapter 2“Overview of principles of hybridization and the strategy of nucleicacid probe assays”, Elsevier, N.Y. (1993); and Current Protocols inMolecular Biology, Chapter 2, Ausubel et al., Eds., Greene Publishingand Wiley-Interscience, New York (1995). Hybridization and/or washconditions can be applied for at least 10, 30, 60, 90, 120, or 240minutes.

“Sequence identity” or “identity” in the context of nucleic acid orpolypeptide sequences refers to the nucleic acid bases or amino acidresidues in two sequences that are the same when aligned for maximumcorrespondence over a specified comparison window.

Thus, “percentage of sequence identity” refers to the value determinedby comparing two optimally aligned sequences over a comparison window,wherein the portion of the polynucleotide or polypeptide sequence in thecomparison window may comprise additions or deletions (i.e., gaps) ascompared to the reference sequence (which does not comprise additions ordeletions) for optimal alignment of the two sequences. The percentage iscalculated by determining the number of positions at which the identicalnucleic acid base or amino acid residue occurs in both sequences toyield the number of matched positions, dividing the number of matchedpositions by the total number of positions in the window of comparisonand multiplying the results by 100 to yield the percentage of sequenceidentity. Useful examples of percent sequence identities include, butare not limited to, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, or 95%,or any integer percentage from 50% to 100%. These identities can bedetermined using any of the programs described herein.

Sequence alignments and percent identity or similarity calculations maybe determined using a variety of comparison methods designed to detecthomologous sequences including, but not limited to, the MegAlign™program of the LASERGENE bioinformatics computing suite (DNASTAR Inc.,Madison, Wis.). Within the context of this application it will beunderstood that where sequence analysis software is used for analysis,that the results of the analysis will be based on the “default values”of the program referenced, unless otherwise specified. As used herein“default values” will mean any set of values or parameters thatoriginally load with the software when first initialized.

The “Clustal V method of alignment” corresponds to the alignment methodlabeled Clustal V (described by Higgins and Sharp, CABIOS. 5:151-153(1989); Higgins, D. G. et al. (1992) Comput. Appl. Biosci. 8:189-191)and found in the MegAlign™ program of the LASERGENE bioinformaticscomputing suite (DNASTAR Inc., Madison, Wis.). For multiple alignments,the default values correspond to GAP PENALTY=10 and GAP LENGTHPENALTY=10. Default parameters for pairwise alignments and calculationof percent identity of protein sequences using the Clustal method areKTUPLE=1, GAP PENALTY=3, WINDOW=5 and DIAGONALS SAVED=5. For nucleicacids these parameters are KTUPLE=2, GAP PENALTY=5, WINDOW=4 andDIAGONALS SAVED=4. After alignment of the sequences using the Clustal Vprogram, it is possible to obtain a “percent identity” by viewing the“sequence distances” table in the same program.

“BLASTN method of alignment” is an algorithm provided by the NationalCenter for Biotechnology Information (NCBI) to compare nucleotidesequences using default parameters.

It is well understood by one skilled in the art that many levels ofsequence identity are useful in identifying polypeptides, from otherspecies, wherein such polypeptides have the same or similar function oractivity. Useful examples of percent identities include, but are notlimited to, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, or 95%, or anyinteger percentage from 50% to 100%. Indeed, any integer amino acididentity from 50% to 100% may be useful in describing the presentinvention, such as 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%,61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%,75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%,89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99%. Also, ofinterest is any full-length or partial complement of this isolatednucleotide fragment.

“Gene” refers to a nucleic acid fragment that expresses a specificprotein, including regulatory sequences preceding (5′ non-codingsequences) and following (3′ non-coding sequences) the coding sequence.“Native gene” refers to a gene as found in nature with its ownregulatory sequences. “Chimeric gene” refers to any gene that is not anative gene, comprising regulatory and coding sequences that are notfound together in nature. Accordingly, a chimeric gene may compriseregulatory sequences and coding sequences that are derived fromdifferent sources, or regulatory sequences and coding sequences derivedfrom the same source, but arranged in a manner different than that foundin nature. A “foreign” gene refers to a gene not normally found in thehost organism, but that is introduced into the host organism by genetransfer. Foreign genes can comprise native genes inserted into anon-native organism, or chimeric genes. A “transgene” is a gene that hasbeen introduced into the genome by a transformation procedure.

The term “genome” as it applies to a plant cells encompasses not onlychromosomal DNA found within the nucleus, but organelle DNA found withinsubcellular components (e.g., mitochondrial, plastid) of the cell.

A “codon-optimized gene” is a gene having its frequency of codon usagedesigned to mimic the frequency of preferred codon usage of the hostcell.

An “allele” is one of several alternative forms of a gene occupying agiven locus on a chromosome. When all the alleles present at a givenlocus on a chromosome are the same that plant is homozygous at thatlocus. If the alleles present at a given locus on a chromosome differthat plant is heterozygous at that locus.

“Coding sequence” refers to a DNA sequence that codes for a specificamino acid sequence. “Regulatory sequences” refer to nucleotidesequences located upstream (5′ non-coding sequences), within, ordownstream (3′ non-coding sequences) of a coding sequence, and whichinfluence the transcription, RNA processing or stability, or translationof the associated coding sequence. Regulatory sequences may include, butare not limited to: promoters, translation leader sequences, introns,polyadenylation recognition sequences, RNA processing sites, effectorbinding sites and stem-loop structures.

“Promoter” refers to a DNA sequence capable of controlling theexpression of a coding sequence or functional RNA. The promoter sequenceconsists of proximal and more distal upstream elements, the latterelements often referred to as enhancers. Accordingly, an “enhancer” is aDNA sequence that can stimulate promoter activity, and may be an innateelement of the promoter or a heterologous element inserted to enhancethe level or tissue-specificity of a promoter. Promoters may be derivedin their entirety from a native gene, or be composed of differentelements derived from different promoters found in nature, or evencomprise synthetic DNA segments. It is understood by those skilled inthe art that different promoters may direct the expression of a gene indifferent tissues or cell types, or at different stages of development,or in response to different environmental conditions. It is furtherrecognized that since in most cases the exact boundaries of regulatorysequences have not been completely defined, DNA fragments of somevariation may have identical promoter activity. Promoters that cause agene to be expressed in most cell types at most times are commonlyreferred to as “constitutive promoters”. New promoters of various typesuseful in plant cells are constantly being discovered; numerous examplesmay be found in the compilation by Okamuro, J. K., and Goldberg, R. B.Biochemistry of Plants 15:1-82 (1989).

“Translation leader sequence” refers to a polynucleotide sequencelocated between the promoter sequence of a gene and the coding sequence.The translation leader sequence is present in the fully processed mRNAupstream of the translation start sequence. The translation leadersequence may affect processing of the primary transcript to mRNA, mRNAstability or translation efficiency. Examples of translation leadersequences have been described (Turner, R. and Foster, G. D., Mol.Biotechnol. 3:225-236 (1995)).

“3′ non-coding sequences”, “transcription terminator” or “terminationsequences” refer to DNA sequences located downstream of a codingsequence and include polyadenylation recognition sequences and othersequences encoding regulatory signals capable of affecting mRNAprocessing or gene expression. The polyadenylation signal is usuallycharacterized by affecting the addition of polyadenylic acid tracts tothe 3′ end of the mRNA precursor. The use of different 3′ non-codingsequences is exemplified by Ingelbrecht, I. L., et al. Plant Cell1:671-680 (1989).

“RNA transcript” refers to the product resulting from RNApolymerase-catalyzed transcription of a DNA sequence. When the RNAtranscript is a perfect complementary copy of the DNA sequence, it isreferred to as the primary transcript. A RNA transcript is referred toas the mature RNA when it is a RNA sequence derived frompost-transcriptional processing of the primary transcript. “MessengerRNA” or “mRNA” refers to the RNA that is without introns and that can betranslated into protein by the cell. “cDNA” refers to a DNA that iscomplementary to, and synthesized from, a mRNA template using the enzymereverse transcriptase. The cDNA can be single-stranded or converted intodouble-stranded form using the Klenow fragment of DNA polymerase I.“Sense” RNA refers to RNA transcript that includes the mRNA and can betranslated into protein within a cell or in vitro. “Antisense RNA”refers to an RNA transcript that is complementary to all or part of atarget primary transcript or mRNA, and that blocks the expression of atarget gene (U.S. Pat. No. 5,107,065). The complementarity of anantisense RNA may be with any part of the specific gene transcript,i.e., at the 5′ non-coding sequence, 3′ non-coding sequence, introns, orthe coding sequence. “Functional RNA” refers to antisense RNA, ribozymeRNA, or other RNA that may not be translated but yet has an effect oncellular processes. The terms “complement” and “reverse complement” areused interchangeably herein with respect to mRNA transcripts, and aremeant to define the antisense RNA of the message.

The term “operably linked” refers to the association of nucleic acidsequences on a single nucleic acid fragment so that the function of oneis regulated by the other. For example, a promoter is operably linkedwith a coding sequence when it is capable of regulating the expressionof that coding sequence (i.e., the coding sequence is under thetranscriptional control of the promoter). Coding sequences can beoperably linked to regulatory sequences in a sense or antisenseorientation. In another example, the complementary RNA regions of theinvention can be operably linked, either directly or indirectly, 5′ tothe target mRNA, or 3′ to the target mRNA, or within the target mRNA, ora first complementary region is 5′ and its complement is 3′ to thetarget mRNA.

Standard recombinant DNA and molecular cloning techniques used hereinare well known in the art and are described more fully in Sambrook, J.,Fritsch, E. F. and Maniatis, T. Molecular Cloning: A Laboratory Manual;Cold Spring Harbor Laboratory: Cold Spring Harbor, N.Y. (1989).Transformation methods are well known to those skilled in the art andare described infra.

“PCR” or “polymerase chain reaction” is a technique for the synthesis oflarge quantities of specific DNA segments and consists of a series ofrepetitive cycles (Perkin Elmer Cetus Instruments, Norwalk, Conn.).Typically, the double-stranded DNA is heat denatured, the two primerscomplementary to the 3′ boundaries of the target segment are annealed atlow temperature and then extended at an intermediate temperature. Oneset of these three consecutive steps is referred to as a “cycle”.

The term “recombinant” refers to an artificial combination of twootherwise separated segments of sequence, e.g., by chemical synthesis orby the manipulation of isolated segments of nucleic acids by geneticengineering techniques.

The terms “plasmid”, “vector” and “cassette” refer to an extrachromosomal element often carrying genes that are not part of thecentral metabolism of the cell, and usually in the form of circulardouble-stranded DNA fragments. Such elements may be autonomouslyreplicating sequences, genome integrating sequences, phage or nucleotidesequences, linear or circular, of a single- or double-stranded DNA orRNA, derived from any source, in which a number of nucleotide sequenceshave been joined or recombined into a unique construction which iscapable of introducing a promoter fragment and DNA sequence for aselected gene product along with appropriate 3′ untranslated sequenceinto a cell. “Transformation cassette” refers to a specific vectorcontaining a foreign gene and having elements in addition to the foreigngene that facilitates transformation of a particular host cell.“Expression cassette” refers to a specific vector containing a foreigngene and having elements in addition to the foreign gene that allow forenhanced expression of that gene in a foreign host (i.e., to a discretenucleic acid fragment into which a nucleic acid sequence or fragment canbe moved.)

The terms “recombinant construct”, “expression construct”, “chimericconstruct”, “construct”, and “recombinant DNA construct” are usedinterchangeably herein. A recombinant construct comprises an artificialcombination of nucleic acid fragments, e.g., regulatory and codingsequences that are not found together in nature. For example, a chimericconstruct may comprise regulatory sequences and coding sequences thatare derived from different sources, or regulatory sequences and codingsequences derived from the same source, but arranged in a mannerdifferent than that found in nature. Such a construct may be used byitself or may be used in conjunction with a vector. If a vector is used,then the choice of vector is dependent upon the method that will be usedto transform host cells as is well known to those skilled in the art.For example, a plasmid vector can be used. The skilled artisan is wellaware of the genetic elements that must be present on the vector inorder to successfully transform, select and propagate host cellscomprising any of the isolated nucleic acid fragments of the invention.The skilled artisan will also recognize that different independenttransformation events will result in different levels and patterns ofexpression (Jones et al., EMBO J. 4:2411-2418 (1985); De Almeida et al.,Mol. Gen. Genetics 218:78-86 (1989)), and thus that multiple events mustbe screened in order to obtain lines displaying the desired expressionlevel and pattern. Such screening may be accomplished by Southernanalysis of DNA, Northern analysis of mRNA expression, immunoblottinganalysis of protein expression, or phenotypic analysis, among others.

The term “expression”, as used herein, refers to the production of afunctional end-product (e.g., a mRNA or a protein [either precursor ormature]).

The term “introduced” means providing a nucleic acid (e.g., expressionconstruct) or protein into a cell. Introduced includes reference to theincorporation of a nucleic acid into a eukaryotic or prokaryotic cellwhere the nucleic acid may be incorporated into the genome of the cell,and includes reference to the transient provision of a nucleic acid orprotein to the cell. Introduced includes reference to stable ortransient transformation methods, as well as sexually crossing. Thus,“introduced” in the context of inserting a nucleic acid fragment (e.g.,a recombinant DNA construct/expression construct) into a cell, means“transfection” or “transformation” or “transduction” and includesreference to the incorporation of a nucleic acid fragment into aeukaryotic or prokaryotic cell where the nucleic acid fragment may beincorporated into the genome of the cell (e.g., chromosome, plasmid,plastid or mitochondrial DNA), converted into an autonomous replicon, ortransiently expressed (e.g., transfected mRNA).

“Mature” protein refers to a post-translationally processed polypeptide(i.e., one from which any pre- or propeptides present in the primarytranslation product have been removed). “Precursor” protein refers tothe primary product of translation of mRNA (i.e., with pre- andpropeptides still present). Pre- and propeptides may be but are notlimited to intracellular localization signals.

“Stable transformation” refers to the transfer of a nucleic acidfragment into a genome of a host organism, including both nuclear andorganellar genomes, resulting in genetically stable inheritance. Incontrast, “transient transformation” refers to the transfer of a nucleicacid fragment into the nucleus, or DNA-containing organelle, of a hostorganism resulting in gene expression without integration or stableinheritance. Host organisms containing the transformed nucleic acidfragments are referred to as “transgenic” organisms.

As used herein, “transgenic” refers to a plant or a cell which compriseswithin its genome a heterologous polynucleotide. Preferably, theheterologous polynucleotide is stably integrated within the genome suchthat the polynucleotide is passed on to successive generations. Theheterologous polynucleotide may be integrated into the genome alone oras part of an expression construct. Transgenic is used herein to includeany cell, cell line, callus, tissue, plant part or plant, the genotypeof which has been altered by the presence of heterologous nucleic acidincluding those transgenics initially so altered as well as thosecreated by sexual crosses or asexual propagation from the initialtransgenic. The term “transgenic” as used herein does not encompass thealteration of the genome (chromosomal or extra-chromosomal) byconventional plant breeding methods or by naturally occurring eventssuch as random cross-fertilization, non-recombinant viral infection,non-recombinant bacterial transformation, non-recombinant transposition,or spontaneous mutation.

“Antisense inhibition” refers to the production of antisense RNAtranscripts capable of suppressing the expression of the target protein.“Co-suppression” refers to the production of sense RNA transcriptscapable of suppressing the expression of identical or substantiallysimilar foreign or endogenous genes (U.S. Pat. No. 5,231,020).Co-suppression constructs in plants previously have been designed byfocusing on overexpression of a nucleic acid sequence having homology toan endogenous mRNA, in the sense orientation, which results in thereduction of all RNA having homology to the overexpressed sequence(Vaucheret et al., Plant J. 16:651-659 (1998); Gura, Nature 404:804-808(2000)). The overall efficiency of this phenomenon is low, and theextent of the RNA reduction is widely variable. More recent work hasdescribed the use of “hairpin” structures that incorporate all, or part,of an mRNA encoding sequence in a complementary orientation that resultsin a potential “stem-loop” structure for the expressed RNA (PCTPublication No. WO 99/53050, published Oct. 21, 1999; PCT PublicationNo. WO 02/00904, published Jan. 3, 2002). This increases the frequencyof co-suppression in the recovered transgenic plants. Another variationdescribes the use of plant viral sequences to direct the suppression, or“silencing”, of proximal mRNA encoding sequences (PCT Publication No. WO98/36083, published Aug. 20, 1998). Both of these co-suppressingphenomena have not been elucidated mechanistically, although geneticevidence has begun to unravel this complex situation (Elmayan et al.,Plant Cell 10:1747-1757 (1998)).

The term “oleaginous” refers to those organisms that tend to store theirenergy source in the form of lipid (Weete, In: Fungal LipidBiochemistry, 2^(nd) Ed., Plenum, 1980). A class of plants identified asoleaginous are commonly referred to as “oilseed” plants. Examples ofoilseed plants include, but are not limited to: soybean (Glycine andSoja sp.), flax (Linum sp.), rapeseed (Brassica sp.), maize, cotton,safflower (Carthamus sp.) and sunflower (Helianthus sp.).

Within oleaginous microorganisms the cellular oil or TAG contentgenerally follows a sigmoid curve, wherein the concentration of lipidincreases until it reaches a maximum at the late logarithmic or earlystationary growth phase and then gradually decreases during the latestationary and death phases (Yongmanitchai and Ward, Appl. Environ.Microbiol. 57:419-25 (1991)). The term “oleaginous yeast” refers tothose microorganisms classified as yeasts that make oil. It is notuncommon for oleaginous microorganisms to accumulate in excess of about25% of their dry cell weight as oil. Examples of oleaginous yeastinclude, but are no means limited to, the following genera: Yarrowia,Candida, Rhodotorula, Rhodosporidium, Cryptococcus, Trichosporon andLipomyces.

The term “Euglenophyceae” refers to a group of unicellular colorless orphotosynthetic flagellates (“euglenoids”) found living in freshwater,marine, soil, and parasitic environments. The class is characterized bysolitary unicells, wherein most are free-swimming and have two flagella(one of which may be nonemergent) arising from an anterior invaginationknown as a reservoir. Photosynthetic euglenoids contain one to manygrass-green chloroplasts, which vary from minute disks to expandedplates or ribbons. Colorless euglenoids depend on osmotrophy orphagotrophy for nutrient assimilation. About 1000 species have beendescribed and classified into about 40 genera and 6 orders. Examples ofEuglenophyceae include, but are no means limited to, the followinggenera: Euglena, Eutreptiella and Tetruetreptia.

The term “plant” refers to whole plants, plant organs, plant tissues,seeds, plant cells, seeds and progeny of the same. Plant cells include,without limitation, cells from seeds, suspension cultures, embryos,meristematic regions, callus tissue, leaves, roots, shoots,gametophytes, sporophytes, pollen and microspores.

“Progeny” comprises any subsequent generation of a plant.

An Overview Microbial Biosynthesis of Fatty Acids and Triacylglycerols

In general, lipid accumulation in oleaginous microorganisms is triggeredin response to the overall carbon to nitrogen ratio present in thegrowth medium. This process, leading to the de novo synthesis of freepalmitate (16:0) in oleaginous microorganisms, is described in detail inPCT Publication No. WO 2004/101757. Palmitate is the precursor oflonger-chain saturated and unsaturated fatty acid derivates, which areformed through the action of elongases and desaturases (FIG. 1).

TAGs (the primary storage unit for fatty acids) are formed by a seriesof reactions that involve: (1) the esterification of one molecule ofacyl-CoA to glycerol-3-phosphate via an acyltransferase to producelysophosphatidic acid; (2) the esterification of a second molecule ofacyl-CoA via an acyltransferase to yield 1,2-diacylglycerol phosphate(commonly identified as phosphatidic acid); (3) removal of a phosphateby phosphatidic acid phosphatase to yield 1,2-diacylglycerol (DAG); and(4) the addition of a third fatty acid by the action of anacyltransferase to form TAG. A wide spectrum of fatty acids can beincorporated into TAGs, including saturated and unsaturated fatty acidsand short-chain and long-chain fatty acids.

Biosynthesis of Omega Fatty Acids

The metabolic process wherein oleic acid is converted to long chainomega-3/omega-6 fatty acids involves elongation of the carbon chainthrough the addition of carbon atoms and desaturation of the moleculethrough the addition of double bonds. This requires a series of specialdesaturation and elongation enzymes present in the endoplasmic reticulummembrane. However, as seen in FIG. 1 and as described below, there areoften multiple alternate pathways for production of a specific longchain omega-3/omega-6 fatty acid.

Specifically, all pathways require the initial conversion of oleic acidto LA, the first of the omega-6 fatty acids, by a delta-12 desaturase.Then, using the “delta-9 elongase/delta-8 desaturase pathway”, longchain omega-6 fatty acids are formed as follows: (1) LA is converted toEDA by a delta-9 elongase; (2) EDA is converted to DGLA by a delta-8desaturase; and (3) DGLA is converted to ARA by a delta-5 desaturase.Alternatively, the “delta-9 elongase/delta-8 desaturase pathway” can beutilized for formation of long chain omega-3 fatty acids as follows: (1)LA is converted to ALA, the first of the omega-3 fatty acids, by adelta-15 desaturase; (2)

ALA is converted to ETrA by a delta-9 elongase; (3) ETrA is converted toETA by a delta-8 desaturase; (4) ETA is converted to EPA by a delta-5desaturase; (5) EPA is converted to DPA by a C_(20/22) elongase; and (6)DPA is converted to DHA by a delta-4 desaturase. Optionally, omega-6fatty acids may be converted to omega-3 fatty acids; for example, ETAand EPA are produced from DGLA and ARA, respectively, by delta-17desaturase activity.

Alternate pathways for the biosynthesis of omega-3/omega-6 fatty acidsutilize a delta-6 desaturase and C_(18/20) elongase (also known asdelta-6 elongase, the terms can be used interchangeably) (i.e., the“delta-6 desaturase/delta-6 elongase pathway”). More specifically, LAand ALA may be converted to GLA and STA, respectively, by a delta-6desaturase; then, a C_(18/20) elongase converts GLA to DGLA and/or STAto ETA.

It is contemplated that the particular functionalities required to beintroduced into a specific host organism for production ofomega-3/omega-6 fatty acids will depend on the host cell (and its nativePUFA profile and/or desaturase/elongase profile), the availability ofsubstrate, and the desired end product(s). For example, expression ofthe delta-9 elongase/delta-8 desaturase pathway may be preferred in someembodiments, as opposed to expression of the delta-6 desaturase/delta-6elongase pathway, since PUFAs produced via the former pathway are devoidof GLA.

One skilled in the art will be able to identify various candidate genesencoding each of the enzymes desired for omega-3/omega-6 fatty acidbiosynthesis. Useful desaturase and elongase sequences may be derivedfrom any source, e.g., isolated from a natural source (from bacteria,algae, fungi, plants, animals, etc.), produced via a semi-syntheticroute or synthesized de novo. Although the particular source of thedesaturase and elongase genes introduced into the host is not critical,considerations for choosing a specific polypeptide having desaturase orelongase activity include: (1) the substrate specificity of thepolypeptide; (2) whether the polypeptide or a component thereof is arate-limiting enzyme; (3) whether the desaturase or elongase isessential for synthesis of a desired PUFA; and/or (4) co-factorsrequired by the polypeptide. The expressed polypeptide preferably hasparameters compatible with the biochemical environment of its locationin the host cell (see PCT Publication No. WO 2004/101757 for additionaldetails).

In additional embodiments, it will also be useful to consider theconversion efficiency of each particular desaturase and/or elongase.More specifically, since each enzyme rarely functions with 100%efficiency to convert substrate to product, the final lipid profile ofunpurified oils produced in a host cell will typically be a mixture ofvarious PUFAs consisting of the desired omega-3/omega-6 fatty acid, aswell as various upstream intermediary PUFAs. Thus, consideration of eachenzyme's conversion efficiency is also a variable when optimizingbiosynthesis of a desired fatty acid that must be considered in light ofthe final desired lipid profile of the product.

With each of the considerations above in mind, candidate genes havingthe appropriate desaturase and elongase activities (e.g., delta-6desaturases, C_(18/20) elongases, delta-5 desaturases, delta-17desaturases, delta-15 desaturases, delta-9 desaturases, delta-12desaturases, C_(14/16) elongases, C_(16/18) elongases, delta-9elongases, delta-8 desaturases, delta-4 desaturases and C_(20/22)elongases) can be identified according to publicly available literature(e.g., GenBank), the patent literature, and experimental analysis oforganisms having the ability to produce PUFAs. These genes will besuitable for introduction into a specific host organism, to enable orenhance the organism's synthesis of PUFAs.

Sequence Identification of Novel Delta-8 Desaturases

In the present invention, nucleotide sequences encoding delta-8desaturases have been isolated from Euglena anabaena (designated hereinas “EaD8Des1”, “EaD8Des2”, “EaD8Des3” and “EaD8Des4”).

Thus, the present invention concerns an isolated polynucleotidecomprising:

-   -   (a) a nucleotide sequence encoding a polypeptide having delta-8        desaturase activity, wherein the polypeptide has at least 80%        amino acid identity, based on the Clustal V method of alignment,        when compared to an amino acid sequence as set forth in SEQ ID        NO:21 [EaD8Des1], SEQ ID NO:22 [EaD8Des2], SEQ ID NO:23        [EaD8Des3] or SEQ ID NO:24 [EaD8Des4];    -   (b) a nucleotide sequence encoding a polypeptide having delta-8        desaturase activity, wherein the nucleotide sequence has at        least 80% sequence identity, based on the BLASTN method of        alignment, when compared to a nucleotide sequence as set forth        in SEQ ID NO:17 [EaD8Des1], SEQ ID NO:18 [EaD8Des2], SEQ ID        NO:19 [EaD8Des3] or SEQ ID NO:20 [EaD8Des4]; or,    -   (c) a complement of the nucleotide sequence of (a) or (b),        wherein the complement and the nucleotide sequence consist of        the same number of nucleotides and are 100% complementary.

In still another aspect, this invention concerns an isolatedpolynucleotide comprising a nucleotide sequence encoding a polypeptidehaving delta-8 desaturase activity, wherein the nucleotide sequence hasat least 90% sequence identity, based on the BLASTN method of alignment,when compared to a nucleotide sequence as set forth in SEQ ID NO:17, SEQID NO:18, SEQ ID NO:19 or SEQ ID NO:20.

In alternate embodiments, the instant EaD8Des1, EaD8Des2, EaD8Des3 orEaD8Des4 desaturase sequences can be codon-optimized for expression in aparticular host organism. As is well known in the art, this can be auseful means to further optimize the expression of the enzyme in thealternate host, since use of host-preferred codons can substantiallyenhance the expression of the foreign gene encoding the polypeptide. Ingeneral, host-preferred codons can be determined within a particularhost species of interest by examining codon usage in proteins(preferably those expressed in the largest amount) and determining whichcodons are used with highest frequency. Then, the coding sequence for apolypeptide of interest having e.g., desaturase activity can besynthesized in whole or in part using the codons preferred in the hostspecies.

In one embodiment of the invention herein, EaD8Des1, EaD8Des2, EaD8Des3and/or EaD8Des4 could be codon-optimized for expression in Yarrowialipolytica, as taught in PCT Publication No. WO 04/101757 and U.S. Pat.No. 7,125,672. In alternate embodiments, it may be desirable to modify aportion of the codons encoding EaD8Des1, EaD8Des2, EaD8Des3 and/orEaD8Des4 (as set forth in SEQ ID NOs:17, 18, 19 and 20, respectively) toenhance expression of the gene in a host organism including, but notlimited to, a plant or plant part.

One skilled in the art would be able to use the teachings herein tocreate various other codon-optimized delta-8 desaturase proteinssuitable for optimal expression in alternate hosts, based on thewildtype EaD8Des1, EaD8Des2, EaD8Des3 and/or EaD8Des4 sequences.Accordingly, the instant invention relates to any codon-optimizeddelta-8 desaturase protein that is derived from the wildtype EaD8Des1(i.e., encoded by SEQ ID NO:17), the wildtype EaD8Des2 (i.e., encoded bySEQ ID NO:18), the wildtype EaD8Des3 (i.e., encoded by SEQ ID NO:19) orthe wildtype EaD8Des4 (i.e., encoded by SEQ ID NO:20).

Identification and Isolation of Homologs

Any of the instant desaturase sequences (i.e., EaD8Des1, EaD8Des2,EaD8Des3 or EaD8Des4) or portions thereof may be used to search fordelta-8 desaturase homologs in the same or other bacterial, algal,fungal, euglenoid or plant species using sequence analysis software. Ingeneral, such computer software matches similar sequences by assigningdegrees of homology to various substitutions, deletions, and othermodifications.

Alternatively, any of the instant desaturase sequences or portionsthereof may also be employed as hybridization reagents for theidentification of delta-8 desaturase homologs. The basic components of anucleic acid hybridization test include a probe, a sample suspected ofcontaining the gene or gene fragment of interest and a specifichybridization method. Probes of the present invention are typicallysingle-stranded nucleic acid sequences that are complementary to thenucleic acid sequences to be detected. Probes are “hybridizable” to thenucleic acid sequence to be detected. Although the probe length can varyfrom 5 bases to tens of thousands of bases, typically a probe length ofabout 15 bases to about 30 bases is suitable. Only part of the probemolecule need be complementary to the nucleic acid sequence to bedetected. In addition, the complementarity between the probe and thetarget sequence need not be perfect. Hybridization does occur betweenimperfectly complementary molecules with the result that a certainfraction of the bases in the hybridized region are not paired with theproper complementary base.

Hybridization methods are well defined. Typically the probe and samplemust be mixed under conditions that will permit nucleic acidhybridization. This involves contacting the probe and sample in thepresence of an inorganic or organic salt under the proper concentrationand temperature conditions. The probe and sample nucleic acids must bein contact for a long enough time that any possible hybridizationbetween the probe and sample nucleic acid may occur. The concentrationof probe or target in the mixture will determine the time necessary forhybridization to occur. The higher the probe or target concentration,the shorter the hybridization incubation time needed. Optionally, achaotropic agent may be added (e.g., guanidinium chloride, guanidiniumthiocyanate, sodium thiocyanate, lithium tetrachloroacetate, sodiumperchlorate, rubidium tetrachloroacetate, potassium iodide, cesiumtrifluoroacetate). If desired, one can add formamide to thehybridization mixture, typically 30-50% (v/v).

Various hybridization solutions can be employed. Typically, thesecomprise from about 20 to 60% volume, preferably 30%, of a polar organicsolvent. A common hybridization solution employs about 30-50% v/vformamide, about 0.15 to 1 M sodium chloride, about 0.05 to 0.1 Mbuffers (e.g., sodium citrate, Tris-HCl, PIPES or HEPES (pH range about6-9)), about 0.05 to 0.2% detergent (e.g., sodium dodecylsulfate), orbetween 0.5-20 mM EDTA, FICOLL (Pharmacia Inc.) (about 300-500 kdal),polyvinylpyrrolidone (about 250-500 kdal), and serum albumin. Alsoincluded in the typical hybridization solution will be unlabeled carriernucleic acids from about 0.1 to 5 mg/mL, fragmented nucleic DNA (e.g.,calf thymus or salmon sperm DNA, or yeast RNA), and optionally fromabout 0.5 to 2% wt/vol glycine. Other additives may also be included,such as volume exclusion agents that include a variety of polarwater-soluble or swellable agents (e.g., polyethylene glycol), anionicpolymers (e.g., polyacrylate or polymethylacrylate) and anionicsaccharidic polymers (e.g., dextran sulfate).

Nucleic acid hybridization is adaptable to a variety of assay formats.One of the most suitable is the sandwich assay format. The sandwichassay is particularly adaptable to hybridization under non-denaturingconditions. A primary component of a sandwich-type assay is a solidsupport. The solid support has adsorbed to it or covalently coupled toit immobilized nucleic acid probe that is unlabeled and complementary toone portion of the sequence.

In additional embodiments, any of the delta-8 desaturase nucleic acidfragments described herein (or any homologs identified thereof) may beused to isolate genes encoding homologous proteins from the same orother bacterial, algal, fungal, euglenoid or plant species. Isolation ofhomologous genes using sequence-dependent protocols is well known in theart. Examples of sequence-dependent protocols include, but are notlimited to: (1) methods of nucleic acid hybridization; (2) methods ofDNA and RNA amplification, as exemplified by various uses of nucleicacid amplification technologies [e.g., polymerase chain reaction (PCR),Mullis et al., U.S. Pat. No. 4,683,202; ligase chain reaction (LCR),Tabor et al., Proc. Acad. Sci. USA 82:1074 (1985); or stranddisplacement amplification (SDA), Walker et al., Proc. Natl. Acad. Sci.U.S.A., 89:392 (1992)]; and (3) methods of library construction andscreening by complementation.

For example, genes encoding similar proteins or polypeptides to thedelta-8 desaturases described herein could be isolated directly by usingall or a portion of the instant nucleic acid fragments as DNAhybridization probes to screen libraries from e.g., any desired yeast orfungus using methodology well known to those skilled in the art (whereinthose organisms producing DGLA and/or ETA would be preferred). Specificoligonucleotide probes based upon the instant nucleic acid sequences canbe designed and synthesized by methods known in the art (Maniatis,supra). Moreover, the entire sequences can be used directly tosynthesize DNA probes by methods known to the skilled artisan (e.g.,random primers DNA labeling, nick translation or end-labelingtechniques), or RNA probes using available in vitro transcriptionsystems. In addition, specific primers can be designed and used toamplify a part of (or full-length of) the instant sequences. Theresulting amplification products can be labeled directly duringamplification reactions or labeled after amplification reactions, andused as probes to isolate full-length DNA fragments under conditions ofappropriate stringency.

Typically, in PCR-type amplification techniques, the primers havedifferent sequences and are not complementary to each other. Dependingon the desired test conditions, the sequences of the primers should bedesigned to provide for both efficient and faithful replication of thetarget nucleic acid. Methods of PCR primer design are common and wellknown in the art (Thein and Wallace, “The use of oligonucleotide asspecific hybridization probes in the Diagnosis of Genetic Disorders”, inHuman Genetic Diseases: A Practical Approach, K. E. Davis Ed., (1986) pp33-50, IRL: Herndon, Va.; and Rychlik, W., In Methods in MolecularBiology, White, B. A. Ed., (1993) Vol. 15, pp 31-39, PCR Protocols:Current Methods and Applications. Humania: Totowa, N.J.).

Generally two short segments of the instant sequences may be used in PCRprotocols to amplify longer nucleic acid fragments encoding homologousgenes from DNA or RNA. PCR may also be performed on a library of clonednucleic acid fragments wherein the sequence of one primer is derivedfrom the instant nucleic acid fragments, and the sequence of the otherprimer takes advantage of the presence of the polyadenylic acid tractsto the 3′ end of the mRNA precursor encoding eukaryotic genes.

Alternatively, the second primer sequence may be based upon sequencesderived from the cloning vector. For example, the skilled artisan canfollow the RACE protocol (Frohman et al., PNAS USA 85:8998 (1988)) togenerate cDNAs by using PCR to amplify copies of the region between asingle point in the transcript and the 3′ or 5′ end. Primers oriented inthe 3′ and 5′ directions can be designed from the instant sequences.Using commercially available 3′ RACE or 5′ RACE systems (Gibco/BRL,Gaithersburg, Md.), specific 3′ or 5′ cDNA fragments can be isolated(Ohara et al., PNAS USA 86:5673 (1989); Loh et al., Science 243:217(1989)).

In other embodiments, any of the delta-8 desaturase nucleic acidfragments described herein (or any homologs identified thereof) may beused for creation of new and improved fatty acid desaturases. As is wellknown in the art, in vitro mutagenesis and selection, chemicalmutagenesis, “gene shuffling” methods or other means can be employed toobtain mutations of naturally occurring desaturase genes. Alternatively,improved fatty acids may be synthesized by domain swapping, wherein afunctional domain from any of the delta-8 desaturase nucleic acidfragments described herein are exchanged with a functional domain in analternate desaturase gene to thereby result in a novel protein. As usedherein, “domain” or “functional domain” refer to nucleic acidsequence(s) that are capable of eliciting a biological response inplants.

Methods for Production of Various Omega-3 and/or Omega-6 Fatty Acids

It is expected that introduction of chimeric genes encoding the delta-8desaturases described herein (i.e., EaD8Des1, EaD8Des2, EaD8Des3,EaD8Des4 or other mutant enzymes, codon-optimized enzymes or homologsthereof), under the control of the appropriate promoters will result inincreased production of DGLA and/or ETA in the transformed hostorganism, respectively. As such, the present invention encompasses amethod for the direct production of PUFAs comprising exposing a fattyacid substrate (i.e., EDA and/or ETrA) to the desaturase enzymesdescribed herein (e.g., EaD8Des1, EaD8Des2, EaD8Des3 or EaD8Des4), suchthat the substrate is converted to the desired fatty acid product (i.e.,DGLA and/or ETA). More specifically, it is an object of the presentinvention to provide a method for the production of DGLA in a host cell(e.g., oleaginous yeast, soybean), wherein the host cell comprises:

-   -   (a) a recombinant construct encoding a delta-8 desaturase        polypeptide selected from the group consisting of SEQ ID NO:21,        SEQ ID NO:22, SEQ ID NO:23 and SEQ ID NO:24; and,    -   (b) a source of EDA;        wherein the host cell is grown under conditions such that the        delta-8 desaturase is expressed and the EDA is converted to        DGLA, and wherein the DGLA is optionally recovered.

In alternate embodiments of the present invention, the delta-8desaturase may be used for the use of the enzyme for the conversion ofETrA to ETA.

Accordingly the invention provides a method for the production of ETA,wherein the host cell comprises:

-   -   (a) a recombinant construct encoding a delta-8 desaturase        polypeptide selected from the group consisting of SEQ ID NO:21,        SEQ ID NO:22, SEQ ID NO:23 and SEQ ID NO:24; and,    -   (b) a source of ETrA;        wherein the host cell is grown under conditions such that the        delta-8 desaturase is expressed and the ETrA is converted to        ETA, and wherein the ETA is optionally recovered.

Alternatively, each delta-8 desaturase gene and its corresponding enzymeproduct described herein can be used indirectly for the production ofvarious omega-6 and omega-3 PUFAs, including e.g., DGLA, ETA, ARA, EPA,DPA and/or DHA (see FIG. 1; see also PCT Publication No. WO2004/101757). Indirect production of omega-3/omega-6 PUFAs occurswherein the fatty acid substrate is converted indirectly into thedesired fatty acid product, via means of an intermediate step(s) orpathway intermediate(s). Thus, it is contemplated that the delta-8desaturases described herein (i.e., EaD8Des1, EaD8Des2, EaD8Des3,EaD8Des4, or other mutant enzymes, codon-optimized enzymes or homologsthereof) may be expressed in conjunction with additional genes encodingenzymes of the PUFA biosynthetic pathway (e.g., delta-6 desaturases,C_(18/20) elongases, delta-17 desaturases, delta-8 desaturases, delta-15desaturases, delta-9 desaturases, delta-12 desaturases, C_(14/16)elongases, C_(16/18) elongases, delta-9 elongases, delta-5 desaturases,delta-4 desaturases, C_(20/22) elongases) to result in higher levels ofproduction of longer-chain omega-3/omega-6 fatty acids (e.g., ARA, EPA,DPA and DHA).

In preferred embodiments, the delta-8 desaturases of the presentinvention will minimally be expressed in conjunction with a delta-9elongase (e.g., a delta-9 elongase or a codon-optimized delta-9elongase). However, the particular genes included within a particularexpression cassette will depend on the host cell (and its PUFA profileand/or desaturase/elongase profile), the availability of substrate andthe desired end product(s).

At times, it may be desirable to minimize by-product fatty acids. Therelative abundance of by-product fatty acids could be decreased byincreasing total delta-8 desaturase activity. One approach to minimizeby-product fatty acids would be to express more than one delta-8desaturase (i.e., the same or different delta-8 desaturase). Forinstance, the presence of sciadonic acid (SCl) and/or juniperonic acid(JUP) [commonly found in the seed lipids of gymnosperms (Wolff et al.,Lipids 35(1):1-22 (2000)), such as those in the Pinaceae family (pine)]might be considered by-product fatty acids of a delta-6desaturase/delta-6 elongase pathway or delta-9-elongase/delta-8desaturase pathway. Although these fatty acids are considered to havevarious health-enhancing properties themselves (Nakane et al., Biol.Pharm. Bull. 23: 758-761 (2000)), their presence as by-product fattyacids in an engineered PUFA pathway, such as in an oilseed crop, may notbe desirable depending on the application.

The term “delta-6 desaturase/delta-6 elongase pathway” also refers to abiosynthetic pathway for production of long-chain PUFAs. This pathway,at a minimum, comprises a delta-6 desaturase and a delta-6 elongase,thereby enabling biosynthesis of DGLA and/or ETA from LA and ALA,respectively. With expression of other desaturases and elongases, ARA,EPA, DPA and DHA may also be synthesized. Occasionally, a delta-6elongase may elongate fatty acids other than the intended fatty acid.For instance, delta-6 elongases generally convert GLA to DGLA but somedelta-6 elongases may also convert unintended substrates such as LA orALA to EDA or ETrA, respectively. In a delta-6 desaturase/delta-6elongase pathway, EDA and ETrA would be considered “by-product fattyacids” as defined below. Addition of a delta-8 desaturase to a delta-6desaturase/delta-6 elongase pathway would provided a means to convertthe “by-product fatty acids” EDA and ETrA back into the “intermediatefatty acids” (as defined previously) DGLA and ETA, respectively.

Plant Expression Systems, Cassettes and Vectors, and Transformation

In one embodiment, this invention concerns a recombinant constructcomprising any one of the delta-8 desaturase polynucleotides of theinvention operably linked to at least one regulatory sequence suitablefor expression in a plant. A promoter is a DNA sequence that directscellular machinery of a plant to produce RNA from the contiguous codingsequence downstream (3′) of the promoter. The promoter region influencesthe rate, developmental stage, and cell type in which the RNA transcriptof the gene is made. The RNA transcript is processed to produce mRNAwhich serves as a template for translation of the RNA sequence into theamino acid sequence of the encoded polypeptide. The 5′ non-translatedleader sequence is a region of the mRNA upstream of the protein codingregion that may play a role in initiation and translation of the mRNA.The 3′ transcription termination/polyadenylation signal is anon-translated region downstream of the protein coding region thatfunctions in the plant cell to cause termination of the RNA transcriptand the addition of polyadenylate nucleotides to the 3′ end of the RNA.

The origin of the promoter chosen to drive expression of the delta-8desaturase coding sequence is not important as long as it has sufficienttranscriptional activity to accomplish the invention by expressingtranslatable mRNA for the desired nucleic acid fragments in the desiredhost tissue at the right time. Either heterologous or non-heterologous(i.e., endogenous) promoters can be used to practice the invention. Forexample, suitable promoters include, but are not limited to: the alphaprime subunit of beta conglycinin promoter, the Kunitz trypsin inhibitor3 promoter, the annexin promoter, the glycinin Gy1 promoter, the betasubunit of beta conglycinin promoter, the P34/Gly Bd m 30K promoter, thealbumin promoter, the Leg A1 promoter and the Leg A2 promoter.

The annexin, or P34, promoter is described in PCT Publication No. WO2004/071178 (published Aug. 26, 2004). The level of activity of theannexin promoter is comparable to that of many known strong promoters,such as: (1) the CaMV 35S promoter (Atanassova et al., Plant Mol. Biol.37:275-285 (1998); Battraw and Hall, Plant Mol. Biol. 15:527-538 (1990);Holtorf et al., Plant Mol. Biol. 29:637-646 (1995); Jefferson et al.,EMBO J. 6:3901-3907 (1987); Wilmink et al., Plant Mol. Biol. 28:949-955(1995)); (2) the Arabidopsis oleosin promoters (Plant et al., Plant Mol.Biol. 25:193-205 (1994); Li, Texas A&M University Ph.D. dissertation,pp. 107-128 (1997)); (3) the Arabidopsis ubiquitin extension proteinpromoters (Callis et al., J. Biol. Chem. 265(21):12486-93 (1990)); (4) atomato ubiquitin gene promoter (Rollfinke et al., Gene. 211(2):267-76(1998)); (5) a soybean heat shock protein promoter (Schoffl et al., MolGen Genet. 217(2-3):246-53 (1989)); and, (6) a maize H3 histone genepromoter (Atanassova et al., Plant Mol. Biol. 37(2):275-85 (1989)).

Another useful feature of the annexin promoter is its expression profilein developing seeds. The annexin promoter is most active in developingseeds at early stages (before 10 days after pollination) and is largelyquiescent in later stages. The expression profile of the annexinpromoter is different from that of many seed-specific promoters, e.g.,seed storage protein promoters, which often provide highest activity inlater stages of development (Chen et al., Dev. Genet. 10:112-122 (1989);Ellerstrom et al., Plant Mol. Biol. 32:1019-1027 (1996); Keddie et al.,Plant Mol. Biol. 24:327-340 (1994); Plant et al., (supra); Li, (supra)).The annexin promoter has a more conventional expression profile butremains distinct from other known seed specific promoters. Thus, theannexin promoter will be a very attractive candidate whenoverexpression, or suppression, of a gene in embryos is desired at anearly developing stage. For example, it may be desirable to overexpressa gene regulating early embryo development or a gene involved in themetabolism prior to seed maturation.

Following identification of an appropriate promoter suitable forexpression of a specific delta-8 desaturase coding sequence, thepromoter is then operably linked in a sense orientation usingconventional means well known to those skilled in the art.

Standard recombinant DNA and molecular cloning techniques used hereinare well known in the art and are described more fully in Sambrook, J.et al., In Molecular Cloning: A Laboratory Manual; 2^(nd) ed.; ColdSpring Harbor Laboratory Press: Cold Spring Harbor, N.Y., 1989(hereinafter “Sambrook et al., 1989”) or Ausubel, F. M., Brent, R.,Kingston, R. E., Moore, D. D., Seidman, J. G., Smith, J. A. and Struhl,K., Eds.; In Current Protocols in Molecular Biology; John Wiley andSons: New York, 1990 (hereinafter “Ausubel et al., 1990”).

Once the recombinant construct has been made, it may then be introducedinto a plant cell of choice by methods well known to those of ordinaryskill in the art (e.g., transfection, transformation andelectroporation). Oilseed plant cells are the preferred plant cells. Thetransformed plant cell is then cultured and regenerated under suitableconditions permitting expression of the long-chain PUFA which is thenoptionally recovered and purified.

The recombinant constructs of the invention may be introduced into oneplant cell; or, alternatively, each construct may be introduced intoseparate plant cells. Expression in a plant cell may be accomplished ina transient or stable fashion as is described above.

The desired long-chain PUFAs can be expressed in seed. Also within thescope of this invention are seeds or plant parts obtained from suchtransformed plants.

Plant parts include differentiated and undifferentiated tissuesincluding, but not limited to the following: roots, stems, shoots,leaves, pollen, seeds, tumor tissue and various forms of cells andculture (e.g., single cells, protoplasts, embryos and callus tissue).The plant tissue may be in plant or in a plant organ, tissue or cellculture.

The term “plant organ” refers to plant tissue or a group of tissues thatconstitute a morphologically and functionally distinct part of a plant.The term “genome” refers to the following: (1) the entire complement ofgenetic material (genes and non-coding sequences) that is present ineach cell of an organism, or virus or organelle; and/or (2) a completeset of chromosomes inherited as a (haploid) unit from one parent.

Thus, this invention also concerns a method for transforming a cell,comprising transforming a cell with the recombinant construct of theinvention and selecting those cells transformed with the recombinantconstruct of claim 8.

Also of interest is a method for producing a transformed plantcomprising transforming a plant cell with the delta-8 desaturasepolynucleotides of the instant invention and regenerating a plant fromthe transformed plant cell.

Methods for transforming dicots (primarily by use of Agrobacteriumtumefaciens) and obtaining transgenic plants have been published, amongothers, for: cotton (U.S. Pat. No. 5,004,863; U.S. Pat. No. 5,159,135);soybean (U.S. Pat. No. 5,569,834; U.S. Pat. No. 5,416,011); Brassica(U.S. Pat. No. 5,463,174); peanut (Cheng et al. Plant Cell Rep.15:653-657 (1996); McKently et al. Plant Cell Rep. 14:699-703 (1995));papaya (Ling, K. et al. Bio/technology 9:752-758 (1991)); and pea (Grantet al. Plant Cell Rep. 15:254-258 (1995)). For a review of othercommonly used methods of plant transformation see Newell, C. A. (Mol.Biotechnol. 16:53-65 (2000)). One of these methods of transformationuses Agrobacterium rhizogenes (Tepfler, M. and Casse-Delbart, F.Microbiol. Sci. 4:24-28 (1987)). Transformation of soybeans using directdelivery of DNA has been published using PEG fusion (PCT Publication No.WO 92/17598), electroporation (Chowrira, G. M. et al., Mol. Biotechnol.3:17-23 (1995); Christou, P. et al., Proc. Natl. Acad. Sci. U.S.A.84:3962-3966 (1987)), microinjection and particle bombardement (McCabe,D. E. et. al., Bio/Technology 6:923 (1988); Christou et al., PlantPhysiol. 87:671-674 (1988)).

There are a variety of methods for the regeneration of plants from planttissue. The particular method of regeneration will depend on thestarting plant tissue and the particular plant species to beregenerated. The regeneration, development and cultivation of plantsfrom single plant protoplast transformants or from various transformedexplants is well known in the art (Weissbach and Weissbach, In: Methodsfor Plant Molecular Biology, (Eds.), Academic: San Diego, Calif.(1988)). This regeneration and growth process typically includes thesteps of selection of transformed cells and culturing thoseindividualized cells through the usual stages of embryonic developmentthrough the rooted plantlet stage. Transgenic embryos and seeds aresimilarly regenerated. The resulting transgenic rooted shoots arethereafter planted in an appropriate plant growth medium such as soil.Preferably, the regenerated plants are self-pollinated to providehomozygous transgenic plants. Otherwise, pollen obtained from theregenerated plants is crossed to seed-grown plants of agronomicallyimportant lines. Conversely, pollen from plants of these important linesis used to pollinate regenerated plants. A transgenic plant of thepresent invention containing a desired polypeptide is cultivated usingmethods well known to one skilled in the art.

In addition to the above discussed procedures, practitioners arefamiliar with the standard resource materials which describe specificconditions and procedures for: the construction, manipulation andisolation of macromolecules (e.g., DNA molecules, plasmids, etc.); thegeneration of recombinant DNA fragments and recombinant expressionconstructs; and, the screening and isolating of clones. See, forexample: Sambrook et al., Molecular Cloning: A Laboratory Manual, ColdSpring Harbor: NY (1989); Maliga et al., Methods in Plant MolecularBiology, Cold Spring Harbor: NY (1995); Birren et al., Genome Analysis:Detecting Genes, Vol. 1, Cold Spring Harbor: NY (1998); Birren et al.,Genome Analysis: Analyzing DNA, Vol. 2, Cold Spring Harbor: NY (1998);Plant Molecular Biology: A Laboratory Manual, eds. Clark, Springer: NY(1997).

Examples of oilseed plants include, but are not limited to: soybean,Brassica species, sunflower, maize, cotton, flax and safflower.

Examples of PUFAs having at least twenty carbon atoms and five or morecarbon-carbon double bonds include, but are not limited to, omega-3fatty acids such as EPA, DPA and DHA. Seeds obtained from such plantsare also within the scope of this invention as well as oil obtained fromsuch seeds.

Thus, in one embodiment this invention concerns an oilseed plantcomprising:

(a) a first recombinant DNA construct comprising an isolatedpolynucleotide encoding a delta-8 desaturase polypeptide, operablylinked to at least one regulatory sequence; and,

(b) at least one additional recombinant DNA construct comprising anisolated polynucleotide, operably linked to at least one regulatorysequence, encoding a polypeptide selected from the group consisting of adelta-4 desaturase, a delta-5 desaturase, a delta-6 desaturase, adelta-8 desaturase, a delta-9 desaturase, a delta-9 elongase, a delta-12desaturase, a delta-15 desaturase, a delta-17 desaturase, a C_(14/16)elongase, a C_(16/18) elongase, a C_(18/20) elongase and a C₂₀₋₂₂elongase.

Such additional desaturases are discussed, for example, in U.S. Pat.Nos. 6,075,183, 5,968,809, 6,136,574, 5,972,664, 6,051,754, 6,410,288and PCT Publication Nos. WO 98/46763, WO 98/46764, WO 00/12720 and WO00/40705.

The choice of combination of cassettes used depends in part on the PUFAprofile and/or desaturase/elongase profile of the oilseed plant cells tobe transformed and the long-chain PUFA which is to be expressed.

In another aspect, this invention concerns a method for makinglong-chain PUFAs in a plant cell comprising:

-   -   (a) transforming a cell with the recombinant construct of the        invention; and,    -   (b) selecting those transformed cells that make long-chain        PUFAs.

In still another aspect, this invention concerns a method for producingat least one PUFA in a soybean cell comprising:

-   -   (a) transforming a soybean cell with a first recombinant DNA        construct comprising:        -   (i) an isolated polynucleotide encoding a delta-8 desaturase            polypeptide, operably linked to at least one regulatory            sequence; and,        -   (ii) at least one additional recombinant DNA construct            comprising an isolated polynucleotide, operably linked to at            least one regulatory sequence, encoding a polypeptide            selected from the group consisting of a delta-4 desaturase,            a delta-5 desaturase, a delta-6 desaturase, a delta-8            desaturase, a delta-9 desaturase, a delta-9 elongase, a            delta-12 desaturase, a delta-15 desaturase, a delta-17            desaturase, a C_(14/16) elongase, a C_(16/18) elongase, a            C_(18/20) elongase and a C_(20/22) elongase;    -   (b) regenerating a soybean plant from the transformed cell of        step (a); and,    -   (c) selecting those seeds obtained from the plants of step (b)        having an altered level of PUFAs when compared to the level in        seeds obtained from a nontransformed soybean plant.

In other preferred embodiments, the at least one additional recombinantDNA construct encodes a polypeptide having delta-9 elongase activity,e.g., the delta-9 elongase isolated or derived from Isochrysis galbana(GenBank Accession No. AF390174; IgD9e) or the delta-9 elongase isolatedor derived from Euglena gracilis as set forth in SEQ ID NO:39.

Microbial Expression Systems, Cassettes and Vectors, and Transformation

The delta-8 desaturase genes and gene products described herein (i.e.,EaD8Des1, EaD8Des2, EaD8Des3, EaD8Des4, or other mutant enzymes,codon-optimized enzymes or homologs thereof) may also be produced inheterologous microbial host cells, particularly in the cells ofoleaginous yeasts (e.g., Yarrowia lipolytica).

Microbial expression systems and expression vectors containingregulatory sequences that direct high level expression of foreignproteins are well known to those skilled in the art. Any of these couldbe used to construct chimeric genes for production of any of the geneproducts of the instant sequences. These chimeric genes could then beintroduced into appropriate microorganisms via transformation to providehigh-level expression of the encoded enzymes.

Vectors or DNA cassettes useful for the transformation of suitablemicrobial host cells are well known in the art. The specific choice ofsequences present in the construct is dependent upon the desiredexpression products (supra), the nature of the host cell and theproposed means of separating transformed cells versus non-transformedcells. Typically, however, the vector or cassette contains sequencesdirecting transcription and translation of the relevant gene(s), aselectable marker and sequences allowing autonomous replication orchromosomal integration. Suitable vectors comprise a region 5′ of thegene that controls transcriptional initiation (e.g., a promoter) and aregion 3′ of the DNA fragment that controls transcriptional termination(i.e., a terminator). It is most preferred when both control regions arederived from genes from the transformed microbial host cell, although itis to be understood that such control regions need not be derived fromthe genes native to the specific species chosen as a production host.

Initiation control regions or promoters which are useful to driveexpression of the instant delta-8 desaturase ORFs in the desiredmicrobial host cell are numerous and familiar to those skilled in theart. Virtually any promoter capable of directing expression of thesegenes in the selected host cell is suitable for the present invention.Expression in a microbial host cell can be accomplished in a transientor stable fashion. Transient expression can be accomplished by inducingthe activity of a regulatable promoter operably linked to the gene ofinterest. Stable expression can be achieved by the use of a constitutivepromoter operably linked to the gene of interest. As an example, whenthe host cell is yeast, transcriptional and translational regionsfunctional in yeast cells are provided, particularly from the hostspecies (e.g., see PCT Publication Nos. WO 2004/101757 and WO2006/052870 for preferred transcriptional initiation regulatory regionsfor use in Yarrowia lipolytica). Any one of a number of regulatorysequences can be used, depending upon whether constitutive or inducedtranscription is desired, the efficiency of the promoter in expressingthe ORF of interest, the ease of construction and the like.

Nucleotide sequences surrounding the translational initiation codon‘ATG’ have been found to affect expression in yeast cells. If thedesired polypeptide is poorly expressed in yeast, the nucleotidesequences of exogenous genes can be modified to include an efficientyeast translation initiation sequence to obtain optimal gene expression.For expression in yeast, this can be done by site-directed mutagenesisof an inefficiently expressed gene by fusing it in-frame to anendogenous yeast gene, preferably a highly expressed gene.Alternatively, one can determine the consensus translation initiationsequence in the host and engineer this sequence into heterologous genesfor their optimal expression in the host of interest.

The termination region can be derived from the 3′ region of the genefrom which the initiation region was obtained or from a different gene.A large number of termination regions are known and functionsatisfactorily in a variety of hosts (when utilized both in the same anddifferent genera and species from where they were derived). Thetermination region usually is selected more as a matter of conveniencerather than because of any particular property. Preferably, when themicrobial host is a yeast cell, the termination region is derived from ayeast gene (particularly Saccharomyces, Schizosaccharomyces, Candida,Yarrowia or Kluyveromyces). The 3′-regions of mammalian genes encodingγ-interferon and α-2 interferon are also known to function in yeast.Termination control regions may also be derived from various genesnative to the preferred hosts. Optionally, a termination site may beunnecessary; however, it is most preferred if included. Although notintended to be limiting, termination regions useful in the disclosureherein include: ˜100 by of the 3′ region of the Yarrowia lipolyticaextracellular protease (XPR; GenBank Accession No. M17741); the acyl-coAoxidase (Aco3: GenBank Accession No. AJ001301 and No. CAA04661; Pox3:GenBank Accession No. XP_(—)503244) terminators; the Pex20 (GenBankAccession No. AF054613) terminator; the Pex16 (GenBank Accession No.U75433) terminator; the Lip1 (GenBank Accession No. Z50020) terminator;the Lip2 (GenBank Accession No. AJ012632) terminator; and the3-oxoacyl-coA thiolase (OCT; GenBank Accession No. X69988) terminator.

As one of skill in the art is aware, merely inserting a gene into acloning vector does not ensure that it will be successfully expressed atthe level needed. In response to the need for a high expression rate,many specialized expression vectors have been created by manipulating anumber of different genetic elements that control aspects oftranscription, translation, protein stability, oxygen limitation andsecretion from the microbial host cell. More specifically, some of themolecular features that have been manipulated to control gene expressioninclude: (1) the nature of the relevant transcriptional promoter andterminator sequences; (2) the number of copies of the cloned gene andwhether the gene is plasmid-borne or integrated into the genome of thehost cell; (3) the final cellular location of the synthesized foreignprotein; (4) the efficiency of translation and correct folding of theprotein in the host organism; (5) the intrinsic stability of the mRNAand protein of the cloned gene within the host cell; and (6) the codonusage within the cloned gene, such that its frequency approaches thefrequency of preferred codon usage of the host cell. Each of these typesof modifications are encompassed in the present invention, as means tofurther optimize expression of the delta-8 desaturases described herein.

Once the DNA encoding a polypeptide suitable for expression in anappropriate microbial host cell (e.g., oleaginous yeast) has beenobtained (e.g., a chimeric gene comprising a promoter, ORF andterminator), it is placed in a plasmid vector capable of autonomousreplication in a host cell, or it is directly integrated into the genomeof the host cell. Integration of expression cassettes can occur randomlywithin the host genome or can be targeted through the use of constructscontaining regions of homology with the host genome sufficient to targetrecombination within the host locus. Where constructs are targeted to anendogenous locus, all or some of the transcriptional and translationalregulatory regions can be provided by the endogenous locus.

In the present invention, the preferred method of expressing genes inYarrowia lipolytica is by integration of linear DNA into the genome ofthe host; and, integration into multiple locations within the genome canbe particularly useful when high level expression of genes are desired[e.g., in the Ura3 locus (GenBank Accession No. AJ306421), the Leu2 genelocus (GenBank Accession No. AF260230), the Lys5 gene (GenBank AccessionNo. M34929), the Aco2 gene locus (GenBank Accession No. AJ001300), thePox3 gene locus (Pox3: GenBank Accession No. XP_(—)503244; or, Aco3:GenBank Accession No. AJ001301), the delta-12 desaturase gene locus (PCTPublication No. WO2004/104167), the Lip1 gene locus (GenBank AccessionNo. Z50020) and/or the Lip2 gene locus (GenBank Accession No.AJ012632)].

Advantageously, the Ura3 gene can be used repeatedly in combination with5-fluoroorotic acid (5-fluorouracil-6-carboxylic acid monohydrate;“5-FOA”) selection (infra), to readily permit genetic modifications tobe integrated into the Yarrowia genome in a facile manner.

Where two or more genes are expressed from separate replicating vectors,it is desirable that each vector has a different means of selection andshould lack homology to the other construct(s) to maintain stableexpression and prevent reassortment of elements among constructs.Judicious choice of regulatory regions, selection means and method ofpropagation of the introduced construct(s) can be experimentallydetermined so that all introduced genes are expressed at the necessarylevels to provide for synthesis of the desired products. Constructscomprising the gene of interest may be introduced into a microbial hostcell by any standard technique. These techniques include transformation(e.g., lithium acetate transformation [Methods in Enzymology,194:186-187 (1991)]), protoplast fusion, bolistic impact,electroporation, microinjection, or any other method that introduces thegene of interest into the host cell. More specific teachings applicablefor oleaginous yeasts (i.e., Yarrowia lipolytica) include U.S. Pat. No.4,880,741 and U.S. Pat. No. 5,071,764 and Chen, D. C. et al. (Appl.Microbiol. Biotechnol., 48(2):232-235 (1997)).

For convenience, a host cell that has been manipulated by any method totake up a DNA sequence (e.g., an expression cassette) will be referredto as “transformed” or “recombinant” herein. The transformed host willhave at least one copy of the expression construct and may have two ormore, depending upon whether the gene is integrated into the genome,amplified or is present on an extrachromosomal element having multiplecopy numbers.

The transformed host cell can be identified by various selectiontechniques, as described in PCT Publication Nos. WO2004/101757 and WO2006/052870.

Preferred selection methods for use herein are resistance to kanamycin,hygromycin and the amino glycoside G418, as well as ability to grow onmedia lacking uracil, leucine, lysine, tryptophan or histidine. Inalternate embodiments, 5-FOA is used for selection of yeast Ura-mutants.The compound is toxic to yeast cells that possess a functioning URA3gene encoding orotidine 5′-monophosphate decarboxylase (OMPdecarboxylase); thus, based on this toxicity, 5-FOA is especially usefulfor the selection and identification of Ura⁻ mutant yeast strains(Bartel, P. L. and Fields, S., Yeast 2-Hybrid System, Oxford University:New York, v. 7, pp 109-147, 1997). More specifically, one can firstknockout the native Ura3 gene to produce a strain having a Ura−phenotype, wherein selection occurs based on 5-FOA resistance. Then, acluster of multiple chimeric genes and a new Ura3 gene can be integratedinto a different locus of the Yarrowia genome to thereby produce a newstrain having a Ura+ phenotype. Subsequent integration produces a newUra3− strain (again identified using 5-FOA selection), when theintroduced Ura3 gene is knocked out. Thus, the Ura3 gene (in combinationwith 5-FOA selection) can be used as a selection marker in multiplerounds of transformation.

Following transformation, substrates suitable for the instant delta-8desaturases (and, optionally other PUFA enzymes that are co-expressedwithin the host cell) may be produced by the host either naturally ortransgenically, or they may be provided exogenously.

Microbial host cells for expression of the instant genes and nucleicacid fragments may include hosts that grow on a variety of feedstocks,including simple or complex carbohydrates, fatty acids, organic acids,oils and alcohols, and/or hydrocarbons over a wide range of temperatureand pH values. Based on the needs of the Applicants' Assignee, the genesdescribed in the instant invention will be expressed in an oleaginousyeast (and in particular Yarrowia lipolytica); however, it iscontemplated that because transcription, translation and the proteinbiosynthetic apparatus is highly conserved, any bacteria, yeast, algaeand/or fungus will be a suitable microbial host for expression of thepresent nucleic acid fragments.

Preferred microbial hosts, however, are oleaginous yeasts. Theseorganisms are naturally capable of oil synthesis and accumulation,wherein the oil can comprise greater than about 25% of the cellular dryweight, more preferably greater than about 30% of the cellular dryweight, and most preferably greater than about 40% of the cellular dryweight. Genera typically identified as oleaginous yeast include, but arenot limited to: Yarrowia, Candida, Rhodotorula, Rhodosporidium,Cryptococcus, Trichosporon and Lipomyces. More specifically,illustrative oil-synthesizing yeasts include: Rhodosporidium toruloides,Lipomyces starkeyii, L. lipoferus, Candida revkaufi, C. pulcherrima, C.tropicalis, C. utilis, Trichosporon pullans, T. cutaneum, Rhodotorulaglutinus, R. graminis, and Yarrowia lipolytica (formerly classified asCandida lipolytica).

Most preferred is the oleaginous yeast Yarrowia lipolytica; and, in afurther embodiment, most preferred are the Y. lipolytica strainsdesignated as ATCC #20362, ATCC #8862, ATCC #18944, ATCC #76982 and/orLGAM S(7)1 (Papanikolaou S., and Aggelis G., Bioresour. Technol.82(1):43-9 (2002)).

Historically, various strains of Y. lipolytica have been used for themanufacture and production of: isocitrate lyase; lipases;polyhydroxyalkanoates; citric acid; erythritol; 2-oxoglutaric acid;γ-decalactone; γ-dodecalatone; and pyruvic acid. Specific teachingsapplicable for engineering ARA, EPA and DHA production in Y. lipolyticaare provided in U.S. patent application Ser. No. 11/264,784 (WO2006/055322), U.S. patent application Ser. No. 11/265,761 (WO2006/052870) and U.S. patent application Ser. No. 11/264,737 (WO2006/052871), respectively.

Other preferred microbial hosts include oleaginous bacteria, algae andother fungi; and, within this broad group of microbial hosts, ofparticular interest are microorganisms that synthesize omega-3/omega-6fatty acids (or those that can be genetically engineered for thispurpose [e.g., other yeast such as Saccharomyces cerevisiae]). Thus, forexample, transformation of Mortierella alpina (which is commerciallyused for production of ARA) with any of the present delta-8 desaturasegenes under the control of inducible or regulated promoters could yielda transformant organism capable of synthesizing increased quantities ofDGLA. The method of transformation of M. alpina is described byMackenzie et al. (Appl. Environ. Microbiol., 66:4655 (2000)). Similarly,methods for transformation of Thraustochytriales microorganisms aredisclosed in U.S. Pat. No. 7,001,772.

Based on the teachings described above, in one embodiment this inventionis drawn to a method of producing either DGLA or ETA, respectively,comprising:

-   -   (a) providing an oleaginous yeast comprising:        -   (i) a first recombinant DNA construct comprising an isolated            polynucleotide encoding a delta-8 desaturase polypeptide,            operably linked to at least one regulatory sequence; and,        -   (ii) a source of desaturase substrate consisting of either            EDA or ETrA, respectively; and,    -   (b) growing the yeast of step (a) in the presence of a suitable        fermentable carbon source wherein the gene encoding the delta-8        desaturase polypeptide is expressed and EDA is converted to DGLA        or ETrA is converted to ETA, respectively; and,    -   (c) optionally recovering the DGLA or ETA, respectively, of step        (b). Substrate feeding may be required.

Of course, since naturally produced PUFAs in oleaginous yeast arelimited to 18:2 fatty acids (i.e., LA), and less commonly, 18:3 fattyacids (i.e., ALA), in more preferred embodiments of the presentinvention the oleaginous yeast will be genetically engineered to expressmultiple enzymes necessary for long-chain PUFA biosynthesis (therebyenabling production of e.g., ARA, EPA, DPA and DHA), in addition to thedelta-8 desaturases described herein.

Specifically, in one embodiment this invention concerns an oleaginousyeast comprising:

(a) a first recombinant DNA construct comprising an isolatedpolynucleotide encoding a delta-8 desaturase polypeptide, operablylinked to at least one regulatory sequence; and,

(b) at least one additional recombinant DNA construct comprising anisolated polynucleotide, operably linked to at least one regulatorysequence, encoding a polypeptide selected from the group consisting of:a delta-4 desaturase, a delta-5 desaturase, delta-6 desaturase, adelta-9 desaturase, a delta-12 desaturase, a delta-15 desaturase, adelta-17 desaturase, a delta-9 elongase, a C_(14/16) elongase, aC_(16/18) elongase, a C_(18/20) elongase and a C_(20/22) elongase.

In particularly preferred embodiments, the at least one additionalrecombinant DNA construct encodes a polypeptide having delta-9 elongaseactivity, e.g., the delta-9 elongase isolated or derived from Isochrysisgalbana (GenBank Accession No. AF390174; IgD9e or IgD9eS) or the delta-9elongase isolated or derived from Euglena gracilis as set forth in SEQID NO:39.

Metabolic Engineering of Omega-3 and/or Omega-6 Fatty Acid Biosynthesisin Microbes

Methods for manipulating biochemical pathways are well known to thoseskilled in the art; and, it is expected that numerous manipulations willbe possible to maximize omega-3 and/or omega-6 fatty acid biosynthesisin oleaginous yeasts, and particularly, in Yarrowia lipolytica. Thismanipulation may require metabolic engineering directly within the PUFAbiosynthetic pathway or additional coordinated manipulation of variousother metabolic pathways.

In the case of manipulations within the PUFA biosynthetic pathway, itmay be desirable to increase the production of LA to enable increasedproduction of omega-6 and/or omega-3 fatty acids. Introducing and/oramplifying genes encoding delta-9 and/or delta-12 desaturases mayaccomplish this. To maximize production of omega-6 unsaturated fattyacids, it is well known to one skilled in the art that production isfavored in a host microorganism that is substantially free of ALA; thus,preferably, the host is selected or obtained by removing or inhibitingdelta-15 or omega-3 type desaturase activity that permits conversion ofLA to ALA. Alternatively, it may be desirable to maximize production ofomega-3 fatty acids (and minimize synthesis of omega-6 fatty acids). Inthis example, one could utilize a host microorganism wherein thedelta-12 desaturase activity that permits conversion of oleic acid to LAis removed or inhibited; subsequently, appropriate expression cassetteswould be introduced into the host, along with appropriate substrates(e.g., ALA) for conversion to omega-3 fatty acid derivatives of ALA(e.g., STA, ETrA, ETA, EPA, DPA, DHA).

In alternate embodiments, biochemical pathways competing with theomega-3 and/or omega-6 fatty acid biosynthetic pathways for energy orcarbon, or native PUFA biosynthetic pathway enzymes that interfere withproduction of a particular PUFA end-product, may be eliminated by genedisruption or down-regulated by other means (e.g., antisense mRNA).

Detailed discussion of manipulations within the PUFA biosyntheticpathway as a means to increase ARA, EPA or DHA (and associatedtechniques thereof) are presented in PCT Publication Nos. WO2006/055322, WO 2006/052870 and WO 2006/052871, respectively, as aredesirable manipulations in the TAG biosynthetic pathway and the TAGdegradation pathway (and associated techniques thereof).

Within the context of the present invention, it may be useful tomodulate the expression of the fatty acid biosynthetic pathway by anyone of the strategies described above. For example, the presentinvention provides methods whereby genes encoding key enzymes in thedelta-9 elongase/delta-8 desaturase biosynthetic pathway are introducedinto oleaginous yeasts for the production of omega-3 and/or omega-6fatty acids. It will be particularly useful to express the present thedelta-8 desaturase genes in oleaginous yeasts that do not naturallypossess omega-3 and/or omega-6 fatty acid biosynthetic pathways andcoordinate the expression of these genes, to maximize production ofpreferred PUFA products using various means for metabolic engineering ofthe host organism.

Microbial Fermentation Processes for PUFA Production

The transformed host cell is grown under conditions that optimizeexpression of chimeric desaturase genes and produce the greatest and themost economical yield of desired PUFAs. In general, media conditionsthat may be optimized include the type and amount of carbon source, thetype and amount of nitrogen source, the carbon-to-nitrogen ratio, theamount of different mineral ions, the oxygen level, growth temperature,pH, length of the biomass production phase, length of the oilaccumulation phase and the time and method of cell harvest. Yarrowialipolytica are generally grown in complex media (e.g., yeastextract-peptone-dextrose broth (YPD)) or a defined minimal media thatlacks a component necessary for growth and thereby forces selection ofthe desired expression cassettes (e.g., Yeast Nitrogen Base (DIFCOLaboratories, Detroit, Mich.)).

Fermentation media in the present invention must contain a suitablecarbon source. Suitable carbon sources are taught in PCT Publication No.WO 2004/101757. Although it is contemplated that the source of carbonutilized in the present invention may encompass a wide variety ofcarbon-containing sources, preferred carbon sources are sugars,glycerol, and/or fatty acids. Most preferred is glucose and/or fattyacids containing between 10-22 carbons.

Nitrogen may be supplied from an inorganic (e.g., (NH₄)₂SO₄) or organic(e.g., urea or glutamate) source. In addition to appropriate carbon andnitrogen sources, the fermentation media must also contain suitableminerals, salts, cofactors, buffers, vitamins and other components knownto those skilled in the art suitable for the growth of the oleaginoushost and promotion of the enzymatic pathways necessary for PUFAproduction. Particular attention is given to several metal ions (e.g.,Mn⁺², Co⁺², Zn⁺², Mg⁺²) that promote synthesis of lipids and PUFAs(Nakahara, T. et al., Ind. Appl. Single Cell Oils, D. J. Kyle and R.Colin, eds. pp 61-97 (1992)).

Preferred growth media in the present invention are common commerciallyprepared media, such as Yeast Nitrogen Base (DIFCO Laboratories,Detroit, Mich.). Other defined or synthetic growth media may also beused and the appropriate medium for growth of the transformant hostcells will be known by one skilled in the art of microbiology orfermentation science. A suitable pH range for the fermentation istypically between about pH 4.0 to pH 8.0, wherein pH 5.5 to pH 7.5 ispreferred as the range for the initial growth conditions. Thefermentation may be conducted under aerobic or anaerobic conditions,wherein microaerobic conditions are preferred.

Typically, accumulation of high levels of PUFAs in oleaginous yeastcells requires a two-stage process, since the metabolic state must be“balanced” between growth and synthesis/storage of fats. Thus, mostpreferably, a two-stage fermentation process is necessary for theproduction of PUFAs in oleaginous yeast (e.g., Yarrowia lipolytica).This approach is described in PCT Publication No. WO 2004/101757, as arevarious suitable fermentation process designs (i.e., batch, fed-batchand continuous) and considerations during growth.

Purification and Processing of PUFA Oils

PUFAs may be found in the host microorganisms and plants as free fattyacids or in esterified forms such as acylglycerols, phospholipids,sulfolipids or glycolipids, and may be extracted from the host cellsthrough a variety of means well-known in the art. One review ofextraction techniques, quality analysis and acceptability standards foryeast lipids is that of Z. Jacobs (Critical Reviews in Biotechnology,12(5/6):463-491 (1992)). A brief review of downstream processing is alsoavailable by A. Singh and O. Ward (Adv. Appl. Microbiol., 45:271-312(1997)).

In general, means for the purification of PUFAs may include extractionwith organic solvents, sonication, supercritical fluid extraction (e.g.,using carbon dioxide), saponification and physical means such aspresses, or combinations thereof. One is referred to the teachings ofPCT Publication No. WO 2004/101757 for additional details. Methods ofisolating seed oils are well known in the art: (Young et al., Processingof Fats and Oils, In The Lipid Handbook, Gunstone et al., eds., Chapter5 pp 253-257; Chapman & Hall: London (1994)). For example, soybean oilis produced using a series of steps involving the extraction andpurification of an edible oil product from the oil-bearing seed. Soybeanoils and soybean byproducts are produced using the generalized stepsshown in Table 3.

TABLE 3 Generalized Steps for Soybean Oil and Byproduct ProductionProcess Impurities Removed and/or Step Process By-Products Obtained # 1soybean seed # 2 oil extraction meal # 3 degumming lecithin # 4 alkalior physical refining gums, free fatty acids, pigments # 5 water washingsoap # 6 bleaching color, soap, metal # 7 (hydrogenation) # 8(winterization) stearine # 9 deodorization free fatty acids,tocopherols, sterols, volatiles # 10  oil products

More specifically, soybean seeds are cleaned, tempered, dehulled andflaked, thereby increasing the efficiency of oil extraction. Oilextraction is usually accomplished by solvent (e.g., hexane) extractionbut can also be achieved by a combination of physical pressure and/orsolvent extraction. The resulting oil is called crude oil. The crude oilmay be degummed by hydrating phospholipids and other polar and neutrallipid complexes that facilitate their separation from the nonhydrating,triglyceride fraction (soybean oil). The resulting lecithin gums may befurther processed to make commercially important lecithin products usedin a variety of food and industrial products as emulsification andrelease (i.e., antisticking) agents. Degummed oil may be further refinedfor the removal of impurities (primarily free fatty acids, pigments andresidual gums). Refining is accomplished by the addition of a causticagent that reacts with free fatty acid to form soap and hydratesphosphatides and proteins in the crude oil. Water is used to wash outtraces of soap formed during refining. The soapstock byproduct may beused directly in animal feeds or acidulated to recover the free fattyacids. Color is removed through adsorption with a bleaching earth thatremoves most of the chlorophyll and carotenoid compounds. The refinedoil can be hydrogenated, thereby resulting in fats with various meltingproperties and textures. Winterization (fractionation) may be used toremove stearine from the hydrogenated oil through crystallization undercarefully controlled cooling conditions. Deodorization (principally viasteam distillation under vacuum) is the last step and is designed toremove compounds which impart odor or flavor to the oil. Other valuablebyproducts such as tocopherols and sterols may be removed during thedeodorization process. Deodorized distillate containing these byproductsmay be sold for production of natural vitamin E and other high-valuepharmaceutical products. Refined, bleached, (hydrogenated, fractionated)and deodorized oils and fats may be packaged and sold directly orfurther processed into more specialized products. A more detailedreference to soybean seed processing, soybean oil production andbyproduct utilization can be found in Erickson, Practical Handbook ofSoybean Processing and Utilization, The American Oil Chemists' Societyand United Soybean Board (1995). Soybean oil is liquid at roomtemperature because it is relatively low in saturated fatty acids whencompared with oils such as coconut, palm, palm kernel and cocoa butter.

Plant and microbial oils containing PUFAs that have been refined and/orpurified can be hydrogenated, to thereby result in fats with variousmelting properties and textures. Many processed fats (including spreads,confectionary fats, hard butters, margarines, baking shortenings, etc.)require varying degrees of solidity at room temperature and can only beproduced through alteration of the source oil's physical properties.This is most commonly achieved through catalytic hydrogenation.

Hydrogenation is a chemical reaction in which hydrogen is added to theunsaturated fatty acid double bonds with the aid of a catalyst such asnickel. For example, high oleic soybean oil contains unsaturated oleic,LA and linolenic fatty acids and each of these can be hydrogenated.Hydrogenation has two primary effects. First, the oxidative stability ofthe oil is increased as a result of the reduction of the unsaturatedfatty acid content. Second, the physical properties of the oil arechanged because the fatty acid modifications increase the melting pointresulting in a semi-liquid or solid fat at room temperature.

There are many variables which affect the hydrogenation reaction, whichin turn alter the composition of the final product. Operating conditionsincluding pressure, temperature, catalyst type and concentration,agitation and reactor design are among the more important parametersthat can be controlled. Selective hydrogenation conditions can be usedto hydrogenate the more unsaturated fatty acids in preference to theless unsaturated ones. Very light or brush hydrogenation is oftenemployed to increase stability of liquid oils. Further hydrogenationconverts a liquid oil to a physically solid fat. The degree ofhydrogenation depends on the desired performance and meltingcharacteristics designed for the particular end product. Liquidshortenings (used in the manufacture of baking products, solid fats andshortenings used for commercial frying and roasting operations) and basestocks for margarine manufacture are among the myriad of possible oiland fat products achieved through hydrogenation. A more detaileddescription of hydrogenation and hydrogenated products can be found inPatterson, H. B. W., Hydrogenation of Fats and Oils: Theory andPractice. The American Oil Chemists'Society (1994).

Hydrogenated oils have become somewhat controversial due to the presenceof trans-fatty acid isomers that result from the hydrogenation process.Ingestion of large amounts of trans-isomers has been linked withdetrimental health effects including increased ratios of low density tohigh density lipoproteins in the blood plasma and increased risk ofcoronary heart disease.

PUFA-Containing Oils for Use in Foodstuffs

The market place currently supports a large variety of food and feedproducts, incorporating omega-3 and/or omega-6 fatty acids (particularlyARA, EPA and DHA). It is contemplated that the plant/seed oils, alteredseeds and microbial oils of the invention comprising PUFAs will functionin food and feed products to impart the health benefits of currentformulations. Compared to other vegetable oils, the oils of theinvention are believed to function similarly to other oils in foodapplications from a physical standpoint (for example, partiallyhydrogenated oils such as soybean oil are widely used as ingredients forsoft spreads, margarine and shortenings for baking and frying).

Plant/seed oils, altered seeds and microbial oils containing omega-3and/or omega-6 fatty acids as described herein will be suitable for usein a variety of food and feed products including, but not limited to:food analogs, meat products, cereal products, baked foods, snack foodsand dairy products. Additionally, the present plant/seed oils, alteredseeds and microbial oils may be used in formulations to impart healthbenefit in medical foods including medical nutritionals, dietarysupplements, infant formula as well as pharmaceutical products. One ofskill in the art of food processing and food formulation will understandhow the amount and composition of the plant and microbial oils may beadded to the food or feed product. Such an amount will be referred toherein as an “effective” amount and will depend on the food or feedproduct, the diet that the product is intended to supplement or themedical condition that the medical food or medical nutritional isintended to correct or treat.

Food analogs can be made using processes well known to those skilled inthe art. There can be mentioned meat analogs, cheese analogs, milkanalogs and the like. Meat analogs made from soybeans contain soyprotein or tofu and other ingredients mixed together to simulate variouskinds of meats. These meat alternatives are sold as frozen, canned ordried foods. Usually, they can be used the same way as the foods theyreplace. Meat alternatives made from soybeans are excellent sources ofprotein, iron and B vitamins. Examples of meat analogs include, but arenot limited to: ham analogs, sausage analogs, bacon analogs, and thelike.

Food analogs can be classified as imitation or substitutes depending ontheir functional and compositional characteristics. For example, animitation cheese need only resemble the cheese it is designed toreplace. However, a product can generally be called a substitute cheeseonly if it is nutritionally equivalent to the cheese it is replacing andmeets the minimum compositional requirements for that cheese. Thus,substitute cheese will often have higher protein levels than imitationcheeses and be fortified with vitamins and minerals.

Milk analogs or nondairy food products include, but are not limited to,imitation milks and nondairy frozen desserts (e.g., those made fromsoybeans and/or soy protein products).

Meat products encompass a broad variety of products. In the UnitedStates “meat” includes “red meats” produced from cattle, hogs and sheep.In addition to the red meats there are poultry items which includechickens, turkeys, geese, guineas, ducks and the fish and shellfish.There is a wide assortment of seasoned and processed meat products:fresh, cured and fried, and cured and cooked. Sausages and hot dogs areexamples of processed meat products. Thus, the term “meat products” asused herein includes, but is not limited to, processed meat products.

A cereal food product is a food product derived from the processing of acereal grain. A cereal grain includes any plant from the grass familythat yields an edible grain (seed). The most popular grains are barley,corn, millet, oats, quinoa, rice, rye, sorghum, triticale, wheat andwild rice. Examples of a cereal food product include, but are notlimited to: whole grain, crushed grain, grits, flour, bran, germ,breakfast cereals, extruded foods, pastas, and the like.

A baked goods product comprises any of the cereal food productsmentioned above and has been baked or processed in a manner comparableto baking (i.e., to dry or harden by subjecting to heat). Examples of abaked good product include, but are not limited to: bread, cakes,doughnuts, bars, pastas, bread crumbs, baked snacks, mini-biscuits,mini-crackers, mini-cookies, and mini-pretzels. As was mentioned above,oils of the invention can be used as an ingredient.

A snack food product comprises any of the above or below described foodproducts.

A fried food product comprises any of the above or below described foodproducts that has been fried.

A health food product is any food product that imparts a health benefit.Many oilseed-derived food products may be considered as health foods.

A beverage can be in a liquid or in a dry powdered form.

For example, there can be mentioned non-carbonated drinks such as fruitjuices, fresh, frozen, canned or concentrate; flavored or plain milkdrinks, etc. Adult and infant nutritional formulas are well known in theart and commercially available (e.g., Similac®, Ensure®, Jevity®, andAlimentum® from Ross Products Division, Abbott Laboratories).

Infant formulas are liquids or reconstituted powders fed to infants andyoung children. “Infant formula” is defined herein as an enteralnutritional product which can be substituted for human breast milk infeeding infants and typically is composed of a desired percentage of fatmixed with desired percentages of carbohydrates and proteins in anaquous solution (e.g., see U.S. Pat. No. 4,670,285). Based on theworldwide composition studies, as well as levels specified by expertgroups, average human breast milk typically contains about 0.20% to0.40% of total fatty acids (assuming about 50% of calories from fat);and, generally the ratio of DHA to ARA would range from about 1:1 to 1:2(see, e.g., formulations of Enfamil LIPIL™ (Mead Johnson & Company) andSimilac Advance™ (Ross Products Division, Abbott Laboratories)). Infantformulas have a special role to play in the diets of infants becausethey are often the only source of nutrients for infants; and, althoughbreast-feeding is still the best nourishment for infants, infant formulais a close enough second that babies not only survive but thrive.

A dairy product is a product derived from milk. A milk analog ornondairy product is derived from a source other than milk, for example,soymilk as was discussed above. These products include, but are notlimited to: whole milk, skim milk, fermented milk products such asyogurt or sour milk, cream, butter, condensed milk, dehydrated milk,coffee whitener, coffee creamer, ice cream, cheese, etc.

Additional food products into which the PUFA-containing oils of theinvention could be included are, for example, chewing gums, confectionsand frostings, gelatins and puddings, hard and soft candies, jams andjellies, white granulated sugar, sugar substitutes, sweet sauces,toppings and syrups, and dry-blended powder mixes.

PUFA-Containing Oils for Use in Health Food Products and Pharmaceuticals

A health food product is any food product that imparts a health benefitand include functional foods, medical foods, medical nutritionals anddietary supplements. Additionally, the plant/seed oils, altered seedsand microbial oils of the invention may be used in standardpharmaceutical compositions (e.g., the long-chain PUFA containing oilscould readily be incorporated into the any of the above mentioned foodproducts, to thereby produce a functional or medical food). Moreconcentrated formulations comprising PUFAs include capsules, powders,tablets, softgels, gelcaps, liquid concentrates and emulsions which canbe used as a dietary supplement in humans or animals other than humans.

PUFA-Containinq Oils for Use in Animal Feeds

Animal feeds are generically defined herein as products intended for useas feed or for mixing in feed for animals other than humans. Theplant/seed oils, altered seeds and microbial oils of the invention canbe used as an ingredient in various animal feeds.

More specifically, although not limited therein, it is expected that theoils of the invention can be used within pet food products, ruminant andpoultry food products and aquacultural food products. Pet food productsare those products intended to be fed to a pet (e.g., dog, cat, bird,reptile, rodent). These products can include the cereal and health foodproducts above, as well as meat and meat byproducts, soy proteinproducts, grass and hay products (e.g., alfalfa, timothy, oat or bromegrass, vegetables). Ruminant and poultry food products are those whereinthe product is intended to be fed to an animal (e.g., turkeys, chickens,cattle, swine). As with the pet foods above, these products can includecereal and health food products, soy protein products, meat and meatbyproducts, and grass and hay products as listed above. Aquaculturalfood products (or “aquafeeds”) are those products intended to be used inaquafarming, i.e., which concerns the propagation, cultivation orfarming of aquatic organisms and/or animals in fresh or marine waters.

EXAMPLES

The present invention is further defined in the following Examples, inwhich parts and percentages are by weight and degrees are Celsius,unless otherwise stated. It should be understood that these Examples,while indicating preferred embodiments of the invention, are given byway of illustration only. From the above discussion and these Examples,one skilled in the art can ascertain the essential characteristics ofthis invention, and without departing from the spirit and scope thereof,can make various changes and modifications of the invention to adapt itto various usages and conditions. Thus, various modifications of theinvention in addition to those shown and described herein will beapparent to those skilled in the art from the foregoing description.Such modifications are also intended to fall within the scope of theappended claims.

The meaning of abbreviations is as follows: “sec” means second(s), “min”means minute(s), “h” means hour(s), “d” means day(s), “μL” meansmicroliter(s), “mL” means milliliter(s), “L” means liter(s), “μM” meansmicromolar, “mM” means millimolar, “M” means molar, “mmol” meansmillimole(s), “pmole” mean micromole(s), “g” means gram(s), “μg” meansmicrogram(s), “ng” means nanogram(s), “U” means unit(s), “bp” means basepair(s) and “kB” means kilobase(s).

General Methods:

Transformation and Cultivation of Yarrowia lipolytica:

Yarrowia lipolytica strains with ATCC Accession Nos. #20362, #76982 and#90812 were purchased from the American Type Culture Collection(Rockville, Md.). Yarrowia lipolytica strains were typically grown at28° C. on YPD agar (1% yeast extract, 2% bactopeptone, 2% glucose, 2%agar).

Transformation of Yarrowia lipolytica was performed according to themethod of Chen, D. C. et al. (Appl. Microbiol. Biotechnol. 48(2):232-235(1997)), unless otherwise noted. Briefly, Yarrowia was streaked onto aYPD plate and grown at 30° C. for approximately 18 h. Several largeloopfuls of cells were scraped from the plate and resuspended in 1 mL oftransformation buffer, comprising: 2.25 mL of 50% PEG, average MW 3350;0.125 mL of 2 M lithium acetate, pH 6.0; 0.125 mL of 2 M DTT; and 50 μgsheared salmon sperm DNA. Then, approximately 500 ng of linearizedplasmid DNA was incubated in 100 μL of resuspended cells, and maintainedat 39° C. for 1 h with vortex mixing at 15 min intervals. The cells wereplated onto selection media plates and maintained at 30° C. for 2 to 3days.

For selection of transformants, minimal medium (“MM”) was generallyused; the composition of MM is as follows: 0.17% yeast nitrogen base(Difco Laboratories, Detroit, Mich.) without ammonium sulfate or aminoacids, 2% glucose, 0.1% proline, pH 6.1). Supplements of uracil wereadded as appropriate to a final concentration of 0.01% (therebyproducing “MMU” selection media, prepared with 20 g/L agar).

Alternatively, transformants were selected on 5-fluoroorotic acid(“FOA”; also 5-fluorouracil-6-carboxylic acid monohydrate) selectionmedia, comprising: 0.17% yeast nitrogen base (Difco Laboratories,Detroit, Mich.) without ammonium sulfate or amino acids, 2% glucose,0.1% proline, 75 mg/L uracil, 75 mg/L uridine, 900 mg/L FOA (ZymoResearch Corp., Orange, Calif.) and 20 g/L agar.

Fatty Acid Analysis of Yarrowia lipolytica:

Unless otherwise stated, for fatty acid analysis cells were collected bycentrifugation and lipids were extracted as described in Bligh, E. G. &Dyer, W. J. (Can. J. Biochem. Physiol. 37:911-917 (1959)). Fatty acidmethyl esters were prepared by transesterification of the lipid extractwith sodium methoxide (Roughan, G. and Nishida I., Arch Biochem Biophys.276(1):38-46 (1990)) and subsequently analyzed with a Hewlett-Packard6890 GC fitted with a 30 m×0.25 mm (i.d.) HP-INNOWAX (Hewlett-Packard)column. The oven temperature was from 170° C. (25 min hold) to 185° C.at 3.5° C./min.

For direct base transesterification, Yarrowia culture (3 mL) washarvested, washed once in distilled water, and dried under vacuum in aSpeed-Vac for 5-10 min. Sodium methoxide (100 μL of 1%) was added to thesample, and then the sample was vortexed and rocked for 20 min. Afteradding 3 drops of 1 M NaCl and 400 μL hexane, the sample was vortexedand spun. The upper layer was removed and analyzed by GC as describedabove.

Example 1 Identification of Delta-8 Desaturase Enzyme Homologs FromEuglena anabaena UTEX 373

The present Example describes the identification of a cDNA fragment (SEQID NO:1) encoding a partial delta-8 desaturase from Euglena anabaenaUTEX 373. This work included the generation of RNA, synthesis of cDNA,generation of a cDNA library and then the identification of a cDNAencoding a partial delta-8 desaturase derived from PCR amplification ofthe cDNA library using degenerate oligonucleotides based on the Euglenagracilis delta-8 desaturase sequence (SEQ ID NO:2; described as Eg5 inPCT Publication No. WO 2006/012325).

Growth of Euglena anabaena UTEX 373 and Preparation of RNA:

Euglena anabaena UTEX 373 was obtained from Dr. Richard Triemer's lab atMichigan State University (East Lansing, Mich.). Approximately 2 mL ofculture was removed for lipid analysis and centrifuged at 1,800×g for 5min. The pellet was washed once with water and re-centrifuged. Theresulting pellet was dried for 5 min under vacuum, resuspended in 100 μLof trimethylsulfonium hydroxide (TMSH) and incubated at room temperaturefor 15 min with shaking. After this, 0.5 mL of hexane was added and thevials were incubated for 15 min at room temperature with shaking. Fattyacid methyl esters (5 μL injected from hexane layer) were separated andquantified using a Hewlett-Packard 6890 Gas Chromatograph fitted with anOmegawax 320 fused silica capillary column (Supelco Inc., Cat. No.24152). The oven temperature was programmed to hold at 170° C. for 1.0min, increase to 240° C. at 5° C./min and then hold for an additional1.0 min. Carrier gas was supplied by a Whatman hydrogen generator.Retention times were compared to those for methyl esters of standardscommercially available (Nu-Chek Prep, Inc. Cat. No. U-99-A) and theresulting chromatogram is shown in FIG. 6. The presence of EDA, ERA, EPAand DHA in the fatty acid profile, with the absence of GLA and STA,suggested that Euglena anabaena uses the delta-9 elongase/delta-8desaturase pathway for LC-PUFA biosynthesis and would be a good sourcefor LC-PUFA biosynthetic genes such as, but not limited to, delta-8desaturases.

The remaining 5 mL of an actively growing culture was transferred into25 mL of AF-6 Medium (Watanabe & Hiroki, NIES-Collection List ofStrains, 5^(th) ed., National Institute for Environmental Studies,Tsukuba, 127 pp (2004)) in a 125 mL glass flask. Euglena anabaenacultures were grown at 22° C. with a 16 h light, 8 h dark cycle for 2weeks with very gentle agitation.

After 2 weeks, the culture (25 mL) was transferred to 100 mL of AF-6medium in a 500 mL glass bottle and the culture was grown for 1 month asdescribed above. After this time, two 50 mL aliquots were transferredinto two separate 500 mL glass bottles containing 250 mL of AF-6 mediumand the cultures were grown for two months as described above (giving atotal of ˜600 mL of culture). After this, the cultures were pelleted bycentrifugation at 1,800×g for 10 min, washed once with water andre-centrifuged. Total RNA was extracted from one of the resultingpellets using the RNA STAT-60™ reagent (TEL-TEST, Inc., Friendswood,Tex.) and following the manufacturer's protocol provided (use 5 mL ofreagent, dissolved RNA in 0.5 mL of water). In this way, 340 μg of totalRNA (680 μg/mL) was obtained from the pellet. The remaining pellet wasfrozen in liquid nitrogen and stored at −80° C. The mRNA was isolatedfrom all 340 μg of total RNA using the mRNA Purification Kit (AmershamBiosciences, Piscataway, N.J.) following the manufacturer's protocolprovided. In this way, 9.0 μg of mRNA was obtained.

Preparation of Euglena anabaena cDNA and Generation of cDNA Libraryeug1c:

A cDNA library was generated using the Cloneminer™ cDNA LibraryConstruction Kit (Cat. No. 18249-029, Invitrogen Corporation, Carlsbad,Calif.) and following the manufacturer's protocol provided (Version B,25-0608). Using the non-radiolabeling method, cDNA was synthesized from5.12 μg of mRNA (described above) using the Biotin-attB2-Oligo(dT)primer. After synthesis of the first and second strand, the attB1adapter was added, ligated and the cDNA was size fractionated usingcolumn chromatography. DNA from fractions were concentrated, recombinedinto pDONR™ 222 and transformed into E. coli ElectroMAX™ DH10B™ T1Phage-Resistant cells (Invitrogen Corporation). The Euglena anabaenalibrary was named eug1c.

The cDNA library eug1c was plated onto LBKan plates (approx. 100,000colonies), the colonies were scraped off and DNA was isolated using theQIAprep® Spin Miniprep Kit (Qiagen Inc., Valencia, Calif.) following themanufacturer's protocol. In this way, a plasmid DNA sub-library fromeug1c was obtained.

Identification of cDNA Fragments Encoding Partial Putative Delta-8Desaturases:

The plasmid DNA sub-library described above was used as template fordegenerate PCR using degenerate primers based on the nucleotide sequenceof the Euglena gracilis delta-8 fatty acid desaturase (SEQ ID NO:2) andthe vector-specific primer pDonor222Eg5-1 (SEQ ID NO:3). The 4degenerate primers used are shown in Table 4.

TABLE 4 Degenerate Oligonucleotides Used to Amplify a Portion of theDelta-8 Desaturase Genes From Euglena anabaena UTEX 373 PrimerNucleotide Sequence SEQ ID NO: D8DEG3-1 RTTRTGNCKATCTTTCCACCA SEQ ID NO:4 D8DEG3-2 RTTRTGNCKGTCTTTCCACCA SEQ ID NO: 5 D8DEG3-3RTTRTGNCKATCCTTCCACCA SEQ ID NO: 6 D8DEG3-4 RTTRTGNCKGTCCTTCCACCA SEQ IDNO: 7

A total of 5 reactions were set up for the cDNA sample. The reactionmixture contained 1 μL of cDNA, 1 μL each of the vector-specific anddegenerate primer (20 μM) and the PCR was carried out using the Phusion™High-Fidelity DNA Polymerase (Cat. No. F553S, Finnzymes Oy, Finland)following the manufacturer's protocol. The resulting DNA fragments werecloned into the pCR-Blunt® cloning vector using the Zero Blunt® PCRCloning Kit (Invitrogen Corporation), following the manufacturer'sprotocol.

Plasmid DNA from the resulting clones was purified using the QIAprep®Spin Miniprep Kit (Qiagen Inc.) following the manufacturer's protocoland DNA inserts were end-sequenced in 384-well plates, usingvector-primed T7 primer (SEQ ID NO:8), M13rev-28 primer (SEQ ID NO:9)with the ABI BigDye version 3 Prism sequencing kit. For the sequencingreaction, 100-200 ng of template and 6.4 pmol of primer were used, andthe following reaction conditions were repeated 25 times: 96° C. for 10sec, 50° C. for 5 sec and 60° C. for 4 min. After ethanol-based cleanup,cycle sequencing reaction products were resolved and detected onPerkin-Elmer ABI 3700 automated sequencers.

A consensus sequence was assembled from the individual sequencesobtained and one representative clone, called pHD23-1 (SEQ ID NO:10)having a sequence identical to the consensus was choosen for furtherstudy.

Identification of the partial cDNA insert in pHD23-1 (SEQ ID NO:1) as apartial delta-8 desaturase was confirmed using BLAST (Basic LocalAlignment Search Tool; Altschul et al., J. Mol. Biol. 215:403-410(1993)) searches for similarity to sequences contained in the BLAST “nr”database (comprising all non-redundant GenBank CDS translations,sequences derived from the 3-dimensional structure Brookhaven ProteinData Bank, the last major release of the SWISS-PROT protein sequencedatabase, EMBL and DDBJ databases). The partial cDNA sequence obtained(SEQ ID NO:1) was translated in all reading frames and compared forsimilarity to all publicly available protein sequences contained in the“nr” database using the BLASTX algorithm (Gish and States, Nat. Genet.3:266-272 (1993)) provided by the NCBI with the default parameter andthe filter turned off. For convenience, the P-value (probability) ofobserving a match of a cDNA sequence to a sequence contained in thesearched databases merely by chance as calculated by BLAST are reportedherein as a “pLog” value, which represents the negative of the logarithmof the reported P-value. Accordingly, the greater the pLog value, thegreater the likelihood that the cDNA sequence and the BLAST “hit”represent homologous proteins.

The BLASTX search using the nucleotide sequence insert from pHD23-1revealed similarity of the protein encoded by the partial cDNA (SEQ IDNO:1) to the Euglena gracilis delta-8 desaturase amino acid sequence(SEQ ID NO:11) (NCBI Accession No. AAD45877(GI 5639724), locus AAD45877,CDS AF139720; Wallis and Browse, Arch. Biochem. Biophys. 365:307-316(1999)) and yielded a pLog value of 63.4 (E value of 4e-63).

Example 2 Isolation of the Full-Length Delta-8 Desaturases from Euglenaanabaena UTEX 373

Approximately 17,000 clones of cDNA library eug1c were plated onto threelarge square (24 cm×24 cm) petri plates (Corning, Corning, N.Y.) eachcontaining LB+50 μg/mL kanamycin agar media. Cells were grown overnightat 37° C. and plates were then cooled to room temperature.

Colony Lifts:

Biodyne B 0.45 μm membrane (Cat. No. 60207, Pall Corporation, Pensacola,Fla.) was trimmed to approximately 22 cm×22 cm and the membrane wascarefully layed on top of the agar to avoid air bubbles. Afterincubation for 2 min at room temperature, the membrane was marked fororientation, lifted off with tweezers and placed colony-side up onfilter paper soaked with 0.5 M sodium hydroxide and 1.5 M sodiumchloride. After denaturation for 4 min, the sodium hydroxide wasneutralized by placing the membrane on filter paper soaked with 0.5 MTris-HCL (pH 7.5) and 1.5 M sodium chloride for 4 min. This step wasrepeated and the membrane was rinsed briefly in 2×SSC buffer (20×SSC is3M sodium chloride, 0.3 M sodium citrate; pH 7.0) and air dried onfilter paper.

Hybridization:

Membranes were pre-hybridized at 65° C. in 200 mL hybridization solutionfor 2 h. Hybridization solution contained 6×SSPE (20×SSPE is 3 M sodiumchloride, 0.2 M sodium phosphate, 20 mM EDTA; pH 7.4), 5×Denhardt'sreagent (100×Denhardt's reagent is 2% (w/v) Ficoll, 2% (w/v)polyvinylpyrrolidone, 2% (w/v) acetylated bovine serum albumin), 0.5%sodium dodecyl sulfate (SDS), 100 μg/mL sheared salmon sperm DNA and 5%dextran sulfate.

A DNA probe was made using an agarose gel purified EcoRI DNA fragment,containing the Euglena anabaena delta-8 desaturase partial DNA fragment,from pHD23-1 (described in Example 1) labeled with P32 dCTP using theRadPrime DNA Labeling System (Cat. No. 18428-011, Invitrogen, Carlsbad,Calif.) following the manufacturer's instructions. Unincorporated P3²dCTP was separated using a NICK column (Cat. No. 17-0855-02, AmershamBiosciences, Piscataway, N.J.) following the manufacturer'sinstructions. The probe was denatured for 5 min at 100° C., placed onice for 3 min and half was added to the hybridization solution.

The membrane was hybridized with the probe overnight at 65° C. withgentle shaking and then washed the following day twice with 2×SSCcontaining 0.5% SDS (5 min each) and twice with 0.2×SSC containing 0.1%SDS (15 min each). After washing, hyperfilm (Cat. No. RPN30K, AmershamBiosciences, Piscataway, N.J.) was exposed to the membrane overnight at−80° C.

Based on alignment of plates with the exposed hyperfilm, positivecolonies were picked using the blunt end of a Pasteur pipette into 1 mLof water and vortexed. Several dilutions were made and plated onto smallround Petri dishes (82 mm) containing LB media plus 50 μg/mL kanamycinto obtain around 100 well isolated colonies on a single plate. Liftswere done as described above except NytranN membrane circles (Cat, No.10416116, Schleicher & Schuell, Keene, N.H.) were used and hybridizationwas carried out in 100 mL using the remaining radiolabeled probe. Inthis way, positive clones were confirmed. Individual positive cloneswere grown at 37° C. in LB+50 μg/mL kanamycin liquid media and plasmidwas purified using the QIAprep® Spin Miniprep Kit (Qiagen Inc.)following the manufacturer's protocol. The plasmid insert was sequencedas described in Example 1 with the ABI BigDye version 3 Prism sequencingkit using vector-primed T7 primer (SEQ ID NO:8), vector-primed M13rev-28primer (SEQ ID NO:9) and the poly(A) tail-primed WobbleToligonucleotides. Briefly, the WobbleT primer is an equimolar mix of 21mer poly(T)A, poly(T)C, and poly(T)G, used to sequence the 3′ end ofcDNA clones. Based on initial sequence data, additional internalfragment sequence was obtained in a similar way using oligonucleotideEaD8seq-1 (SEQ ID NO:12). In this way, the full insert sequences of theeug1c delta-8 desaturase clones were obtained.

Sequences were aligned and compared using Sequencher™ (Version 4.2, GeneCodes Corporation, Ann Arbor, Mich.) and in this way, the clones couldbe categorized into one of four distinct groups based on insert sequence(called EaD8Des1 to EaD8Des4). Representative clones containing the cDNAfor each class of sequence were chosen for further study and sequencesfor each representative plasmid (pLF118-1, pLF118-2, pLF118-3 andpLF118-4) are shown in SEQ ID NO:13, SEQ ID NO:14, SEQ ID NO:15 and SEQID NO:16, respectively. The sequence shown by a string of NNNN'srepresents a region of the polyA tail which was not sequenced. Thecoding sequences for EaD8Des1, EaD8Des2, EaD8Des3 and EaD8Des4 are shownin SEQ ID NO:17, SEQ ID NO:18, SEQ ID NO:19 and SEQ ID NO:20,respectively. The corresponding amino acid sequences for EaD8Des1,EaD8Des2, EaD8Des3 and EaD8Des4 are shown in SEQ ID NO:21, SEQ ID NO:22,SEQ ID NO:23 and SEQ ID NO:24, respectively.

Example 3 Primary Sequence Analysis of the Delta-8 Desaturase Sequencesof Euglena anabaena UTEX 373 and Comparison to a Delta-8 DesaturaseSequence of Euglena gracilis

The amino acid sequences for EaD8Des1 (SEQ ID NO:21), EaD8Des2 (SEQ IDNO:22), EaD8Des3 (SEQ ID NO:23) and EaD8Des4 (SEQ ID NO:24) werecompared using the Clustal W method (using the MegAlign™ v6.1 program ofthe LASARGENE bioinformatics computing suite (DNASTAR Inc.) with thedefault parameters for multiple alignment (GAP PENALTY=10, GAP LENGTHPENALTY=0.2, Delay Divergen Seqs(%)=30, DNA Transition Weight=0.5,Protein Weight Matrix=Gonnet Series, DNA Weight Matrix=IUB).

Compared to the EaD8Des1 (SEQ ID NO:21), EaD8Des2 (SEQ ID NO:22) has 3amino acid substitutions (T110S, M223I & K251T; based on numbering forEaD8Des1), EaD8Des3 (SEQ ID NO:23) has 2 amino acid substitutions (T110S& K251T) and EaD8Des4 (SEQ ID NO:24) has 1 amino acid substitution(T110S).

The amino acid sequences for EaD8Des1 (SEQ ID NO:21), EaD8Des2 (SEQ IDNO:22), EaD8Des3 (SEQ ID NO:23) and EaD8Des4 (SEQ ID NO:24) wereevaluated by BLASTP (Basic Local Alignment Search Tool; Altschul et al.,J. Mol. Biol. 215:403-410 (1993)) searches for similarity to sequencescontained in the BLAST “nr” database (comprising all non-redundantGenBank CDS translations, sequences derived from the 3-dimensionalstructure Brookhaven Protein Data Bank, the last major release of theSWISS-PROT protein sequence database, EMBL and DDBJ databases) usingdefault parameters and the filter off. For convenience, the P-value(probability) of observing a match of a cDNA sequence to a sequencecontained in the searched databases merely by chance as calculated byBLAST are reported herein as “pLog” values, which represent the negativeof the logarithm of the reported P-value. Accordingly, the greater thepLog value, the greater the likelihood that the cDNA sequence and theBLAST “hit” represent homologous proteins.

All four sequences yielded a pLog value of 177 (P value of e-177) versusthe Euglena gracilis delta-8 desaturase amino acid sequence (SEQ IDNO:11) (NCBI Accession No. AAD45877(GI 5639724), locus AAD45877, CDSAF139720; Wallis and Browse, Arch. Biochem. Biophys. 365:307-316 (1999))when compared to the “nr” database. BLAST scores and probabilitiesindicate that the instant nucleic acid fragments encode entire Euglenaanabaena delta-8 fatty acid desaturases.

The amino acid sequences for EaD8Des1 (SEQ ID NO:21), EaD8Des2 (SEQ IDNO:22), EaD8Des3 (SEQ ID NO:23) and EaD8Des4 (SEQ ID NO:24) were thencompared to the corrected Euglena gracilis delta-8 desaturase amino acidsequence (EgD8; SEQ ID NO:25; described as Eg5 in PCT Application No. WO2006/012325) using BlastP (default parameters, filter off), Clustal Vand the Jotun Hein methods of sequence comparison and the % identityusing each method is shown in Table 5. The Clustal V alignment of thesefive amino acid sequences can be seen in FIGS. 7A, 7B and 7C. FIG. 8 isa chart setting forth a comparison of the percent identity (and percentdivergence in the lower half triangle), among the five delta-8desaturase sequences aligned in FIGS. 7A, 7B and 7C.

Sequence percent identity calculations performed by the Clustal V method(Higgins, D. G. and Sharp, P. M., Comput. Appl. Biosci. 5:151-153(1989); Higgins et al., Comput. Appl. Biosci. 8:189-191 (1992)) weredone using the MegAlign™ v6.1 program of the LASERGENE bioinformaticscomputing suite (DNASTAR Inc., Madison, Wis.) with the defaultparameters for pairwise alignment (KTUPLE=1, GAP PENALTY=3, WINDOW=5 andDIAGONALS SAVED=5 and GAP LENGTH PENALTY=10). Sequence percent identitycalculations performed by the Jotun Hein method (Hein, J. J., Meth. Enz.183:626-645 (1990)) were done using the MegAlign™ v6.1 program of theLASERGENE bioinformatics computing suite (DNASTAR Inc., Madison, Wis.)with the default parameters for pairwise alignment (KTUPLE=2).

TABLE 5 Sequence Comparison of EaD8Des1 (SEQ ID NO: 21), EaD8Des2 (SEQID NO: 22), EaD8Des3 (SEQ ID NO: 23) and EaD8Des4 (SEQ ID NO: 24) toEgD8 (SEQ ID NO: 25) % Identity to % Identity to EgD8 % Identity to EgD8(SEQ ID EgD8 (SEQ ID NO: 25) NO: 25) by (SEQ ID NO: 25) by the JotunHein the Clustal V Desaturase by BLASTP Method Method EaD8Des1 73% 74.4%72.1% (SEQ ID NO: 21) EaD8Des2 73% 74.2% 71.9% (SEQ ID NO: 22) EaD8Des373% 74.2% 71.9% (SEQ ID NO: 23) EaD8Des4 73% 74.2% 71.9% (SEQ ID NO: 24)

Example 4 Functional Analysis of the Euglena gracilis UTEX 373 Delta-8Desaturases in Yarrowia lipolytica

The present Example describes functional analysis of the four EaD8Des inYarrowia lipolytica. This work included the following steps: (1) PCRamplification of the EaD8Des with appropriate restriction sites forcloning from plasmids described in Example 2; (2) cloning of the EaD8DesPCR products into cloning vector pCR-Blunt® (Invitrogen Corporation) toproduce pY120-1 to pY120-4; (3) cloning of the EaD8Des genes intoYarrowia expression vector pY115 to produce pY175, pY176, pY177 andpY178; and, (4) comparison of lipid profiles within transformantorganisms comprising pY175, pY176, pY177 and pY178, after substratefeeding.

PCR Amplification of the EaD8Des Genes:

In order to introduce NotI and NcoI restriction sites at the 5′ end ofthe coding sequences and a NotI site at the 3′ end of the codingsequences, each of the EaD8Des genes were PCR amplified. The codingsequences for EaD8Des1 (SEQ ID NO:17), EaD8Des2 (SEQ ID NO:18), EaD8Des3(SEQ ID NO:19) and EaD8Des4 (SEQ ID NO:20) were amplified from pLF118-1(SEQ ID NO:13), pLF118-2 (SEQ ID NO:14), pLF118-3 (SEQ ID NO:15) andpLF118-4 (SEQ ID NO:16), respectively, with oligonucleotide primersEaD8-5 (SEQ ID NO:26) and EaD8-3 (SEQ ID NO:27) using the Phusion™High-Fidelity DNA Polymerase (Cat. No. F553S, Finnzymes Oy, Finland)following the manufacturer's protocol. The resulting DNA fragments werecloned into the pCR-Blunt® cloning vector using the Zero Blunt® PCRCloning Kit (Invitrogen Corporation), following the manufacturer'sprotocol, to produce pLF120-1 (SEQ ID NO:28), pLF120-2 (SEQ ID NO:29),pLF120-3 (SEQ ID NO:30) and pLF120-4 (SEQ ID NO:31), respectively.

sConstruction of Yarrowia Expression Vector pY115, pY175, pY176, pY177and pY178:

Plasmid pY5-30 (which was previously described in PCT Publication No. WO2005/003310; the contents of which are hereby incorporated byreference), is a shuttle plasmid that can replicate both in E. coli andYarrowia lipolytica. Plasmid pY5-30 contains the following: a Yarrowiaautonomous replication sequence (ARS18); a ColE1 plasmid origin ofreplication; an ampicillin-resistance gene (AmpR), for selection in E.coli; a Yarrowia LEU2 gene, for selection in Yarrowia; and a chimericTEF::GUS::XPR gene. Plasmid pDMW263 (SEQ ID NO:32) was created frompY5-30, by replacing the TEF promoter with the Yarrowia lipolyticaFBAINm promoter (PCT Publication No. WO 2005/049805) using techniqueswell known to one skilled in the art. Briefly, this promoter refers to amodified promoter which is located in the 5′ upstream untranslatedregion in front of the ‘ATG’ translation initiation codon of thefructose-bisphosphate aldolase enzyme (E. G. 4.1.2.13) encoded by thefba1 gene and that is necessary for expression, plus a portion of 5′coding region that has an intron, wherein FBAINm has a 52 by deletionbetween the ATG translation initiation codon and the intron of the FBAINpromoter (thereby including only 22 amino acids of the N-terminus) and anew translation consensus motif after the intron. Table 6 summarizes thecomponents of pDMW263 (SEQ ID NO:32).

TABLE 6 Components of Plasmid pDMW263 RE Sites and Nucleotides WithinDescription of Fragment and SEQ ID NO: 32 Chimeric Gene Components4992-4296 ARS18 sequence (GenBank Accession No. A17608) SaII/SacIIFBAINm::GUS::XPR, comprising: (8505-2014) FBAINm: FBAINm promoter (WO2005/049805) GUS: E. coli gene encoding β-glucuronidase (Jefferson, R.A. Nature. 14: 342: 837-838 (1989) XPR: ~100 bp of the 3′ region of theYarrowia Xpr gene (GenBank Accession No. M17741) 6303-8505 Yarrowia Leu2gene (GenBank Accession No. AF260230)

The NcoI/SalI DNA fragment from pDMW263 (SEQ ID NO:32), containing theYarrowia lipolytica FBAINm promoter, was cloned into the NcoI/SalI DNAfragment of pDMW237 (SEQ ID NO:33), previously described in PCTPublication No. WO 2006/012325 (the contents of which are herebyincorporated by reference), containing a synthetic delta-9 elongase genederived from Isochrysis galbana and codon-optimized for expression inYarrowia lipolytica, to produce pY115 (SEQ ID NO:34; FIG. 2). In FIG. 2,the modified FBAINm promoter is called FBA1+Intron. It is alsoFBA1+Intron in other figures, as well as YAR FBA1 PRO+Intron and theseterms are used interchangeably with FBAINm.

The NcoI/NotI DNA fragments from pLF120-1 (SEQ ID NO:28), pLF120-2 (SEQID NO:29), pLF120-3 (SEQ ID NO:30) and pLF120-4 (SEQ ID NO:31),containing each EaD8Des, were cloned into the NcoI/NotI DNA fragmentfrom pY115, containing the Yarrowia lipolytica FBAINm promoter, toproduce pY175 (SEQ ID NO:35; FIG. 3A), pY176 (SEQ ID NO:36; FIG. 3B),pY177 (SEQ ID NO:37; FIG. 3C) and pY178 (SEQ ID NO:38; FIG. 3D),respectively.

Functional Analysis of the Four EaD8Des Genes in Yarrowia lipolytica:

Strain Y2224 was isolated in the following manner: Yarrowia lipolyticaATCC #20362 cells from a YPD agar plate (1% yeast extract, 2%bactopeptone, 2% glucose, 2% agar) were streaked onto a MM plate (75mg/L each of uracil and uridine, 6.7 g/L YNB with ammonia sulfate,without amino acid, and 20 g/L glucose) containing 250 mg/L 5-FOA (ZymoResearch). Plates were incubated at 28° C. and four of the resultingcolonies were patched separately onto MM plates containing 200 mg/mL5-FOA and MM plates lacking uracil and uridine to confirm uracil Ura3auxotrophy.

Strain Y2224 was transformed with pY175 (SEQ ID NO:35; FIG. 3A), pY176(SEQ ID NO:36; FIG. 3B), pY177 (SEQ ID NO:7; FIG. 3C) and pY178 (SEQ IDNO:38; FIG. 3D) as described in the General Methods.

Single colonies of transformant Yarrowia lipolytica containingpY175-pY178 were grown in 3 mL minimal media lacking uracil supplementedwith 0.2% tergitol at 30° C. for 1 day. After this, 0.1 mL wastransferred to 3 mL of the same medium supplemented with eicosadienoicacid [EDA—20:2(11,14)] or eicosatrienoic acid [ERA—20:3(11,14,17)] to0.175 mM. These were incubated for 16 h at 30° C., 250 rpm and thenpellets were obtained by centrifugation. Cells were washed once withwater, pelleted by centrifugation and air dried. Pellets weretransesterified (Roughan, G. and Nishida, I., Arch. Biochem. Biophys.276(1):38-46 (1990)) with 500 μL of 1% sodium methoxide for 30 min. at50° C. after which 500 μL of 1M sodium chloride and 100 μL of heptanewere added. After thorough mixing and centrifugation, fatty acid methylesters (FAMEs) were analyzed by GC. FAMEs (5 μL injected from hexanelayer) were separated and quantified using a Hewlett-Packard 6890 GasChromatograph fitted with an Omegawax 320 fused silica capillary column(Cat. No. 24152, Supelco Inc.). The oven temperature was programmed tohold at 220° C. for 2.6 min, increase to 240° C. at 20° C./min and thenhold for an additional 2.4 min. Carrier gas was supplied by a Whatmanhydrogen generator. Retention times were compared to those for methylesters of standards commercially available (Nu-Chek Prep, Inc.).

The fatty acid profiles for Yarrowia lipolytica expressing pY175-pY178are shown in FIG. 4. Percent C20 desaturation (C20% delta-8 desat) wascalculated either by dividing the wt. % for DGLA by the sum of the wt. %for EDA and DGLA and multiplying by 100 to express as a % or by dividingthe wt. % for ETA by the sum of the wt. % for ERA and DTA andmultiplying by 100 to express as a %, depending on which substrate wasfed (EDA or ERA). Averages are indicated by Ave. followed by appropriateheader. The ratio of desaturation of EDA to ERA is calculated bydividing the Ave. C20% delta-8 desat for EDA by that of ERA.

All of the Euglena anabaena delta-8 desaturases function similarly wellin Yarrowia and convert approximately 50% of the EDA to DGLA. Thereappears to be a slight preference for the EDA over ERA with a EDA/ERAratio of 1.1 to 1.2.

Example 5 Construction of Soybean Expression Vector pKR1152 forCo-Expression of the Euglena anabaena UTEX 373 Delta-8 Desaturase(EaD8Des3) with a Delta-9 Elongase Derived from Euglena qracilis (EqD9e)

The present Example describes construction of a soybean vector forco-expression of EaD8Des3 with EgD9e.

Euglena gracilis Delta-9 Elongase (EgD9e):

A clone from the Euglena cDNA library (eeglc), called eeg1c.pk001.n5f,containing the Euglena gracilis delta-9 elongase (EgD9e; SEQ ID NO:39;which is described in U.S. application Ser. No. 11/601,563 (filed Nov.,16, 2006, which published May 24, 2007; Attorney Docket No. BB-1562) thecontents of which are hereby incorporated by reference) was used astemplate to amplifiy EgD9elo with oligonucleotide primers oEugEL1-1 (SEQID NO:40) and oEugEL1-2 (SEQ ID NO:41) using the VentR® DNA Polymerase(Cat. No. MO254S, New England Biolabs Inc., Beverly, Mass.) followingthe manufacturer's protocol. The resulting DNA fragment was cloned intothe pCR-Blunt® cloning vector using the Zero Blunt® PCR Cloning Kit(Invitrogen Corporation), following the manufacturer's protocol, toproduce pKR906 (SEQ ID NO:42).

A starting plasmid pKR72 (ATCC Accession No. PTA-6019; SEQ ID NO:43,7085 by sequence), a derivative of pKS123 which was previously describedin PCT Publication No. WO 02/008269 (the contents of which are herebyincorporated by reference), contains the hygromycin B phosphotransferasegene (HPT) (Gritz, L. and Davies, J., Gene 25:179-188 (1983)), flankedby the T7 promoter and transcription terminator (T7prom/HPT/T7termcassette), and a bacterial origin of replication (ori) for selection andreplication in bacteria (e.g., E. coli). In addition, pKR72 alsocontains HPT, flanked by the 35S promoter (Odell et al., Nature313:810-812 (1985)) and NOS 3′ transcription terminator (Depicker etal., J. Mol. Appl. Genet. 1:561-570 (1982)) (35S/HPT/NOS3′ cassette) forselection in plants such as soybean. pKR72 also contains a NotIrestriction site, flanked by the promoter for the α′ subunit ofβ-conglycinin (Beachy et al., EMBO J. 4:3047-3053 (1985)) and the 3′transcription termination region of the phaseolin gene (Doyle et al., J.Biol. Chem. 261:9228-9238 (1986)), thus allowing for strongtissue-specific expression in the seeds of soybean of genes cloned intothe NotI site.

EgD9e was released from pKR906 (SEQ ID NO:42) by digestion with NotI andcloned into the NotI site of pKR72 (SEQ ID NO:43) to produce pKR912 (SEQID NO:44). In some instances, pKR912 is referred to as pKR1010 but theyare identical.

Euglena anabaena UTEX 373 Delta-8 desaturase (EaD8Des3):

Vector pKR457 (SEQ ID NO:45), which was previously described in PCTPublication No. WO 2005/047479 (the contents of which are herebyincorporated by reference), contains a NotI site flanked by the Kunitzsoybean Trypsin Inhibitor (KTi) promoter (Jofuku et al., Plant Cell1:1079-1093 (1989)) and the KTi 3′ termination region, the isolation ofwhich is described in U.S. Pat. No. 6,372,965, followed by the soyalbumin transcription terminator, which was previously described in PCTPublication No. WO 2004/071467 (Kti/NotI/Kti3′Salb3′ cassette).

The NotI fragment of pLF120-3 (SEQ ID NO:30), containing the EaD8Des3gene was cloned into the NotI site of pKR457 (SEQ ID NO:45), to producepKR1138 (SEQ ID NO:46).

The BsiWI fragment from pKR1138 (SEQ ID NO:46), containing the EaD8Des3gene, was cloned into the BsiWI site of pKR912 (SEQ ID NO:44) to producepKR1152 (SEQ ID NO:47; FIG. 5). In FIG. 5, the Euglena gracilis delta-9elongase (EgD9e) is called eug el1.

Example 6 Production and Model System Transformation of Somatic SoybeanEmbryo Cultures with Soybean Expression Vectors and Plant RegenerationCulture Conditions:

Soybean embryogenic suspension cultures (cv. Jack) are maintained in 35mL liquid medium SB196 (infra) on a rotary shaker, 150 rpm, 26° C. withcool white fluorescent lights on 16:8 hr day/night photoperiod at lightintensity of 60-85 μE/m2/s. Cultures are subcultured every 7 days to twoweeks by inoculating approximately 35 mg of tissue into 35 mL of freshliquid SB196 (the preferred subculture interval is every 7 days).

Soybean embryogenic suspension cultures are transformed with the soybeanexpression plasmids by the method of particle gun bombardment (Klein etal., Nature 327:70 (1987)) using a DuPont Biolistic PDS1000/HEinstrument (helium retrofit) for all transformations.

Soybean Embryogenic Suspension Culture Initiation:

Soybean cultures are initiated twice each month with 5-7 days betweeneach initiation. Pods with immature seeds from available soybean plantsare picked 45-55 days after planting. Seeds are removed from the podsand placed into a sterilized magenta box. The soybean seeds aresterilized by shaking them for 15 min in a 5% Clorox solution with 1drop of Ivory soap (i.e., 95 mL of autoclaved distilled water plus 5 mLClorox and 1 drop of soap, mixed well). Seeds are rinsed using 2 1-literbottles of sterile distilled water and those less than 4 mm are placedon individual microscope slides. The small end of the seed is cut andthe cotyledons pressed out of the seed coat. When cultures are beingprepared for production transformation, cotyledons are transferred toplates containing SB1 medium (25-30 cotyledons per plate). Plates arewrapped with fiber tape and are maintained at 26° C. with cool whitefluorescent lights on 16:8 h day/night photoperiod at light intensity of60-80 pE/m2/s for eight weeks, with a media change after 4 weeks. Whencultures are being prepared for model system expemiments, cotyledons aretransferred to plates containing SB199 medium (25-30 cotyledons perplate) for 2 weeks, and then transferred to SB1 for 2-4 weeks. Light andtemperature conditions are the same as described above. After incubationon SB1 medium, secondary embryos are cut and placed into SB196 liquidmedia for 7 days.

Preparation of DNA for Bombardment:

Either an intact plasmid or a DNA plasmid fragment containing the genesof interest and the selectable marker gene are used for bombardment.Fragments from soybean expression plasmids are obtained by gel isolationof digested plasmids. In each case, 100 μg of plasmid DNA is used in 0.5mL of the specific enzyme mix described below. Plasmids are digestedwith AscI (100 units) in NEBuffer 4 (20 mM Tris-acetate, 10 mM magnesiumacetate, 50 mM potassium acetate, 1 mM dithiothreitol, pH 7.9), 100μg/mL BSA, and 5 mM beta-mercaptoethanol at 37° C. for 1.5 h. Theresulting DNA fragments are separated by gel electrophoresis on 1%SeaPlaque GTG agarose (BioWhitaker Molecular Applications) and the DNAfragments containing gene cassettes are cut from the agarose gel. DNA ispurified from the agarose using the GELase digesting enzyme followingthe manufacturer's protocol.

A 50 μL aliquot of sterile distilled water containing 3 mg of goldparticles (3 mg gold) is added to 30 μL of a 10 ng/μL DNA solution(either intact plasmid or DNA fragment prepared as described herein), 25μL 5M CaCl₂ and 20 μL of 0.1 M spermidine. The mixture is shaken 3 minon level 3 of a vortex shaker and spun for 10 sec in a bench microfuge.The supernatant is removed, followed by a wash with 400 μL 100% ethanoland another brief centrifugation. The 400 μL ethanol is removed and thepellet is resuspended in 40 μL of 100% ethanol. Five μL of DNAsuspension is dispensed to each flying disk of the Biolistic PDS1000/HEinstrument disk. Each 5 μL aliquot contains approximately 0.375 mg goldper bombardment (e.g., per disk).

For model system transformations, the protocol is identical except for afew minor changes (i.e., 1 mg of gold particles is added to 5 μL of a 1μg/μL DNA solution, 50 μL of a 2.5M CaCl₂ is used and the pellet isultimately resuspended in 85 μL of 100% ethanol thus providing 0.058 mgof gold particles per bombardment).

Tissue Preparation and Bombardment with DNA:

Approximately 150-200 mg of seven day old embryogenic suspensioncultures is placed in an empty, sterile 60×15 mm petri dish and the dishis covered with plastic mesh. The chamber is evacuated to a vacuum of27-28 inches of mercury, and tissue is bombarded one or two shots perplate with membrane rupture pressure set at 1100 PSI. Tissue is placedapproximately 3.5 inches from the retaining/stopping screen. Modelsystem transformation conditions are identical except 100-150 mg ofembryogenic tissue is used, rupture pressure is set at 650 PSI andtissue is place approximately 2.5 inches from the retaining screen.

Selection of Transformed Embryos:

Transformed embryos are selected either using hygromycin (when thehygromycin B phosphotransferase (HPT) gene is used as the selectablemarker) or chlorsulfuron (when the acetolactate synthase (ALS) gene isused as the selectable marker).

Following bombardment, the tissue is placed into fresh SB196 media andcultured as described above. Six to eight days post-bombardment, theSB196 is exchanged with fresh SB196 containing either 30 mg/L hygromycinor 100 ng/mL chlorsulfuron, depending on the selectable marker used. Theselection media is refreshed weekly. Four to six weeks post-selection,green, transformed tissue is observed growing from untransformed,necrotic embryogenic clusters.

Embryo Maturation:

For production transformations, isolated, green tissue is removed andinoculated into multiwell plates to generate new, clonally propagated,transformed embryogenic suspension cultures. Transformed embryogenicclusters are cultured for four-six weeks in multiwell plates at 26° C.in SB196 under cool white fluorescent (Phillips cool white EconowattF40/CW/RS/EW) and Agro (Phillips F40 Agro) bulbs (40 watt) on a 16:8 hrphotoperiod with light intensity of 90-120 μE/m²s. After this timeembryo clusters are removed to a solid agar media, SB166, for one-twoweeks and then subcultured to SB103 medium for 3-4 weeks to matureembryos. After maturation on plates in SB103, individual embryos areremoved from the clusters, dried and screened for alterations in theirfatty acid compositions as described in Example 7.

For model system transformations, embryos are matured in soybeanhistodifferentiation and maturation liquid medium (SHaM liquid media;Schmidt et al., Cell Biology and Morphogenesis 24:393 (2005)) using amodified procedure. Briefly, after 4 weeks of selection in SB196 asdescribed above, embryo clusters are removed to 35 mL of SB228 (SHaMliquid media) in a 250 mL Erlenmeyer flask. Tissue is maintained in SHaMliquid media on a rotary shaker at 130 rpm and 26° C. with cool whitefluorescent lights on a 16:8 hr day/night photoperiod at a lightintensity of 60-85 μE/m2/s for 2 weeks as embryos mature. Embryos grownfor 2 weeks in SHaM liquid media are equivalent in size and fatty acidcontent to embryos cultured on SB166/SB103 for 5-8 weeks.

After maturation in SHaM liquid media, individual embryos are removedfrom the clusters, dried and screened for alterations in their fattyacid compositions as described in Example 7.

Media Recipes: SB 196-FN Lite Liquid Proliferation Medium (Per Liter)

MS FeEDTA - 100x Stock 1 10 mL MS Sulfate - 100x Stock 2 10 mL FN LiteHalides - 100x Stock 3 10 mL FN Lite P, B, Mo - 100x Stock 4 10 mL B5vitamins (1 mL/L) 1.0 mL 2,4-D (10 mg/L final concentration) 1.0 mL KNO₃2.83 gm (NH₄)₂SO₄ 0.463 gm asparagine 1.0 gm sucrose (1%) 10 gm pH 5.8

FN Lite Stock Solutions

Stock Number 1000 mL 500 mL 1 MS Fe EDTA 100x Stock Na₂ EDTA* 3.724 g1.862 g FeSO₄—7H₂O 2.784 g 1.392 g 2 MS Sulfate 100x stock MgSO₄—7H₂O37.0 g 18.5 g MnSO₄—H₂O 1.69 g 0.845 g ZnSO₄—7H₂O 0.86 g 0.43 gCUSO₄—5H₂O 0.0025 g 0.00125 g 3 FN Lite Halides 100x Stock CaCl₂—2H₂O30.0 g 15.0 g KI 0.083 g 0.0715 g CoCl₂—6H₂O 0.0025 g 0.00125 g 4 FNLite P, B, Mo 100x Stock KH₂PO₄ 18.5 g 9.25 g H₃BO₃ 0.62 g 0.31 gNa₂MoO₄—2H₂O 0.025 g 0.0125 g *Add first, dissolve in dark bottle whilestirring

SB1 Solid Medium (Per Liter)

-   -   1 package MS salts (Gibco/BRL Cat. No. 11117-066)    -   1 mL B5 vitamins 1000× stock    -   31.5 g glucose    -   2 mL 2,4-D (20 mg/L final concentration)    -   pH 5.7    -   8 g TC agar

SB199 Solid Medium (Per Liter)

-   -   1 package MS salts (Gibco/BRL Cat. No. 11117-066)    -   1 mL B5 vitamins 1000× stock    -   30 g Sucrose    -   4 ml 2,4-D (40 mg/L final concentration)    -   pH 7.0    -   2 gm Gelrite

SB 166 Solid Medium (Per Liter)

-   -   1 package MS salts (Gibco/BRL Cat. No. 11117-066)    -   1 mL B5 vitamins 1000× stock    -   60 g maltose    -   750 mg MgCl₂ hexahydrate    -   5 g activated charcoal    -   pH 5.7    -   2 g gelrite

SB 103 Solid Medium (Per Liter)

-   -   1 package MS salts (Gibco/BRL Cat. No. 11117-066)    -   1 mL B5 vitamins 1000× stock    -   60 g maltose    -   750 mg MgCl2 hexahydrate    -   pH 5.7    -   2 g gelrite

SB 71-4 Solid Medium (Per Liter)

-   -   1 bottle Gamborg's B5 salts w/sucrose (Gibco/BRL Cat. No.        21153-036)    -   pH 5.7    -   5 g TC agar

2,4-D Stock

Obtain premade from Phytotech Cat. No. D 295—concentration 1 mg/mL

B5 Vitamins Stock (per 100 mL)

Store aliquots at −20° C.

-   -   10 g myo-inositol    -   100 mg nicotinic acid    -   100 mg pyridoxine HCl    -   1 g thiamine        If the solution does not dissolve quickly enough, apply a low        level of heat via the hot stir plate.

SB 228—Soybean Histodifferentiation & Maturation (SHaM) (Per Liter)

DDI H₂O 600 mL FN-Lite Macro Salts for SHaM 10X 100 mL MS Micro Salts1000x 1 mL MS FeEDTA 100x 10 mL CaCl 100x 6.82 mL B5 Vitamins 1000x 1 mLL-Methionine 0.149 g Sucrose 30 g Sorbitol 30 g Adjust volume to 900 mLpH 5.8 Autoclave Add to cooled media (≦30° C.): *Glutamine (finalconcentration 30 mM) 4% 110 mL *Note: Final volume will be 1010 mL afterglutamine addition.Since glutamine degrades relatively rapidly, it may be preferable to addimmediately prior to using media. Expiration 2 weeks after glutamine isadded; base media can be kept longer w/o glutamine.

FN-lite Macro for SHAM 10×—Stock #1 (Per Liter)

(NH₄)2SO₄ (ammonium sulfate) 4.63 g KNO₃ (potassium nitrate) 28.3 gMgSO₄*7H₂0 (magnesium sulfate heptahydrate) 3.7 g KH₂PO₄ (potassiumphosphate, monobasic) 1.85 g Bring to volume Autoclave

MS Micro 1000×—Stock #2 (Per 1 Liter)

H₃BO₃ (boric acid) 6.2 g MnSO₄*H₂O (manganese sulfate monohydrate) 16.9g ZnSO4*7H20 (zinc sulfate heptahydrate) 8.6 g Na₂MoO₄*2H20 (sodiummolybdate dihydrate) 0.25 g CuSO₄*5H₂0 (copper sulfate pentahydrate)0.025 g CoCl₂*6H₂0 (cobalt chloride hexahydrate) 0.025 g KI (potassiumiodide) 0.8300 g Bring to volume Autoclave

FeEDTA 100×—Stock #3 (Per Liter)

Na₂EDTA* (sodium EDTA) 3.73 g FeSO₄*7H₂0 (iron sulfate heptahydrate)2.78 g *EDTA must be completely dissolved before adding iron. Bring toVolume Solution is photosensitive. Bottle(s) should be wrapped in foilto omit light. Autoclave

Ca 100×—Stock #4 (Per Liter)

CaCl₂*2H₂0 (calcium chloride dihydrate) 44 g Bring to Volume Autoclave

B5 Vitamin 1000×—Stock #5 (Per Liter)

Thiamine*HCl 10 g  Nicotinic Acid 1 g Pyridoxine*HCl 1 g Myo-Inositol100 g  Bring to Volume Store frozen

4% Glutamine—Stock #6 (Per Liter)

DDI water heated to 30° C. 900 mL L-Glutamine  40 g Gradually add whilestirring and applying low heat. Do not exceed 35° C. Bring to VolumeFilter Sterilize Store frozen* *Note: Warm thawed stock in 31° C. bathto fully dissolve crystals.

Regeneration of Soybean Somatic Embryos Into Plants:

In order to obtain whole plants from embryogenic suspension cultures,the tissue must be regenerated. Embyros are matured as described inabove. After subculturing on medium SB103 for 3 weeks, individualembryos can be removed from the clusters and screened for alterations intheir fatty acid compositions as described in Example 7. It should benoted that any detectable phenotype, resulting from the expression ofthe genes of interest, could be screened at this stage. This wouldinclude, but not be limited to, alterations in fatty acid profile,protein profile and content, carbohydrate content, growth rate,viability, or the ability to develop normally into a soybean plant.

Matured individual embryos are desiccated by placing them into an empty,small petri dish (35×10 mm) for approximately 4 to 7 days. The platesare sealed with fiber tape (creating a small humidity chamber).Desiccated embryos are planted into SB71-4 medium where they are left togerminate under the same culture conditions described above. Germinatedplantlets are removed from germination medium and rinsed thoroughly withwater and then are planted in Redi-Earth in 24-cell pack tray, coveredwith clear plastic dome. After 2 weeks the dome is removed and plantshardened off for a further week. If plantlets looked hardy they aretransplanted to 10″ pot of Redi-Earth with up to 3 plantlets per pot.After 10 to 16 weeks, mature seeds are harvested, chipped and analyzedfor fatty acids.

Example 7 Fatty Acid Analysis of Transgenic Somatic Soybean Embryos

Mature somatic soybean embryos are a good model for zygotic embryos.While in the globular embryo state in liquid culture, somatic soybeanembryos contain very low amounts of triacylglycerol or storage proteinstypical of maturing, zygotic soybean embryos. At this developmentalstage, the ratio of total triacylglyceride to total polar lipid(phospholipids and glycolipid) is about 1:4, as is typical of zygoticsoybean embryos at the developmental stage from which the somatic embryoculture was initiated. At the globular stage as well, the mRNAs for theprominent seed proteins, α′-subunit of β-conglycinin, kunitz trypsininhibitor 3, and seed lectin are essentially absent. Upon transfer tohormone-free media to allow differentiation to the maturing somaticembryo state, triacylglycerol becomes the most abundant lipid class. Aswell, mRNAs for α′-subunit of β-conglycinin, kunitz trypsin inhibitor 3and seed lectin become very abundant messages in the total mRNApopulation. On this basis, the somatic soybean embryo system behavesvery similarly to maturing zygotic soybean embryos in vivo, and is thusa good and rapid model system for analyzing the phenotypic effects ofmodifying the expression of genes in the fatty acid biosynthesis pathway(see PCT Publication No. WO 2002/00904, more specifically Example 3).Most importantly, the model system is also predictive of the fatty acidcomposition of seeds from plants derived from transgenic embryos.

A subset of soybean embryos for each event generated from eitherproduction transformation or model system transformation (as describedin Example 6) are harvested in the following way. Embryos (5-10 embryos)from each event are picked into glass GC vials and fatty acid methylesters are prepared by transesterification. For transesterification, 50μL of trimethylsulfonium hydroxide (TMSH) and 0.5 mL of hexane is addedto the embryos in glass vials and incubated for 30 min at roomtemperature while shaking. Fatty acid methyl esters (5 μL injected fromhexane layer) are separated and quantified using a Hewlett-Packard 6890Gas Chromatograph fitted with an Omegawax 320 fused silica capillarycolumn (Cat. No. 24152, Supelco Inc.). The oven temperature isprogrammed to hold at 220° C. for 2.6 min, increase to 240° C. at 20°C./min and then hold for an additional 2.4 min. Carrier gas is suppliedby a Whatman hydrogen generator. Retention times are compared to thosefor methyl esters of standards commercially available (Nu-Chek Prep,Inc.). Events having good phenotype can be re-analyzed by GC usingidentical conditions except the oven temperature is held at 150° C. for1 min and then increased to 240° C. at 5° C.

Example 8 Construction of Alternate Soybean Expression Vectors gorExpression of Euglena anabaena UTEX 373 Delta-8 Desaturases (EaD8Des1-4)

In addition to the genes, promoters, terminators and gene cassettesdescribed herein, one skilled in the art can appreciate that otherpromoter/gene/terminator cassette combinations can be synthesized in away similar to, but not limited to, that described herein for expressionof EaD8Des3. Similarly, it may be desirable to express other PUFA genes(such as those described below in Table 9), for co-expression with anyof the delta-8 desaturases of the present invention.

For instance, PCT Publication Nos. WO 2004/071467 and WO 2004/071178describe the isolation of a number of promoter and transcriptionterminator sequences for use in embryo-specific expression in soybean.Furthermore, PCT Publication Nos. WO 2004/071467, WO 2005/047479 and WO2006/012325 describe the synthesis of multiple promoter/gene/terminatorcassette combinations by ligating individual promoters, genes andtranscription terminators together in unique combinations. Generally, aNotI site flanked by the suitable promoter (such as those listed in, butnot limited to, Table 7) and a transcription terminator (such as thoselisted in, but not limited to, Table 8) is used to clone the desiredgene. NotI sites can be added to a gene of interest such as those listedin, but not limited to, Table 9 using PCR amplification witholigonucleotides designed to introduce NotI sites at the 5′ and 3′ endsof the gene. The resulting PCR product is then digested with NotI andcloned into a suitable promoter/NotI/terminator cassette.

In addition, PCT Publication Nos. WO 2004/071467, WO 2005/047479 and WO2006/012325 describe the further linking together of individual genecassettes in unique combinations, along with suitable selectable markercassettes, in order to obtain the desired phenotypic expression.Although this is done mainly using different restriction enzymes sites,one skilled in the art can appreciate that a number of techniques can beutilized to achieve the desired promoter/gene/transcription terminatorcombination. In so doing, any combination of embryo-specificpromoter/gene/transcription terminator cassettes can be achieved. Oneskilled in the art can also appreciate that these cassettes can belocated on individual DNA fragments or on multiple fragments whereco-expression of genes is the outcome of co-transformation of multipleDNA fragments.

TABLE 7 Seed-specific Promoters Promoter Organism Promoter Referenceβ-conglycinin α′-subunit soybean Beachy et al., EMBO J. 4: 3047-3053(1985) kunitz trypsin inhibitor soybean Jofuku et al., Plant Cell 1:1079-1093 (1989) Annexin soybean WO 2004/071467 glycinin Gy1 soybean WO2004/071467 albumin 2S soybean U.S. Pat. No. 6,177,613 legumin A1 peaRerie et al., Mol. Gen. Genet. 225: 148-157 (1991) β-conglycininβ-subunit soybean WO 2004/071467 BD30 (also called P34) soybean WO2004/071467 legumin A2 pea Rerie et al., Mol. Gen. Genet. 225: 148-157(1991)

TABLE 8 Transcription Terminators Transcription Terminator OrganismReference phaseolin 3′ bean WO 2004/071467 kunitz trypsin inhibitor 3′soybean WO 2004/071467 BD30 (also called P34) 3′ soybean WO 2004/071467legumin A2 3′ pea WO 2004/071467 albumin 2S 3′ soybean WO 2004/071467

TABLE 9 PUFA Biosynthetic Pathway Genes Gene Organism Reference delta-6desaturase Saprolegnia diclina WO 2002/081668 delta-6 desaturaseMortierella alpina U.S. Pat. No. 5,968,809 elongase Mortierella alpinaWO 2000/12720 U.S. Pat. No. 6,403,349 delta-5 desaturase Mortierellaalpina U.S. Pat. No. 6,075,183 delta-5 desaturase Saprolegnia diclina WO2002/081668 delta-5 desaturase Peridinium sp. U.S. Patent ApplicationNo. 11/748,637 delta-5 desaturase Euglena gracilis U.S. PatentApplication No. 11/748,629 delta-15 desaturase Fusarium moniliforme WO2005/047479 delta-17 desaturase Saprolegnia diclina WO 2002/081668elongase Thraustochytrium WO 2002/08401 aureum U.S. Pat. No. 6,677,145elongase Pavlova sp. Pereira et al., Biochem. J. 384: 357-366 (2004)delta-4 desaturase Schizochytrium WO 2002/090493 aggregatum U.S. Pat.No. 7,045,683 delta-4 desaturase Isochrysis galbana WO 2002/090493 U.S.Pat. No. 7,045,683 delta-4 desaturase Thraustochytrium WO 2002/090493aureum U.S. Pat. No. 7,045,683 delta-4 desaturase Euglena gracilis U.S.Patent Application No. 10/552,127 delta-9 elongase Isochrysis galbana WO2002/077213 delta-9 elongase Euglena gracilis U.S. Patent ApplicationNo. 11/601,563 delta-9 elongase Eutreptiella sp. U.S. Patent ApplicationNo. CCMP389 11/601,564 delta-8 desaturase Euglena gracilis WO 2000/34439U.S. Pat. No. 6,825,017 WO 2004/057001 WO 2006/012325 delta-8 desaturaseAcanthamoeba Sayanova et al., FEBS Lett. castellanii 580: 1946-1952(2006) delta-8 desaturase Pavlova salina WO 2005/103253 delta-8desaturase Pavlova lutheri U.S. Patent Application No. 11/737,772delta-8 desaturase Tetruetreptia U.S. Patent Application No.pomquetensis 11/876,115 CCMP1491 delta-8 desaturase Eutreptiella sp.U.S. Patent Application No. CCMP389 11/876,115 delta-8 desaturaseEutreptiella U.S. Patent Application No. cf_gymnastica 11/876,115CCMP1594

Example 9 Synthesis of a Codon-Optimized Delta-8 Desaturase Gene forYarrowia lipolytica (EaD8S)

The codon usage of the delta-8 desaturase gene (EaD8Des3; SEQ ID NO:19)of Euglena anabaena was optimized for expression in Yarrowia lipolytica,in a manner similar to that described in PCT Publication No. WO2004/101753. Specifically, a codon-optimized delta-8 desaturase gene(designated “EaD8S”, SEQ ID NO:48) was designed based on the codingsequence of EaD8Des3 (SEQ ID NOs:19 and 23), according to the Yarrowiacodon usage pattern (PCT Publication No. WO 2004/101753), the consensussequence around the ‘ATG’ translation initiation codon, and the generalrules of RNA stability (Guhaniyogi, G. and J. Brewer, Gene,265(1-2):11-23 (2001)). In addition to modification of the translationinitiation site, 231 by of the 1260 by coding region were modified(18.3%) and 208 codons were optimized (49.5%). The GC content wasreduced from 56.8% within the wild type gene (i.e., EaD8Des3) to 54.8%within the synthetic gene (i.e., EaD8S). A NcoI site and NotI sites wereincorporated around the translation initiation codon and after the stopcodon of EaD8S (SEQ ID NO:48), respectively. FIGS. 9A and 9B shows acomparison of the nucleotide sequences of EaD8Des3 (SEQ ID NO:19) andEaD8S (SEQ ID NO:48). The codon optimized EaD8S gene did not change anyamino acid sequence of EaD8Des3 (SEQ ID NO:23). The designed EaD8S genewas synthesized by GenScript Corporation (Piscataway, N.J.) and clonedinto pUC57 (GenBank Accession No. Y14837) to generate pEaD8S (SEQ IDNO:49; FIG. 10).

Based on the teachings herein concerning vector construction andsuitable promoter and terminators for use in Yarrowia lipolytica, one ofskill in the art will be able to construct additional plasmids suitablefor expression of EaD8S (SEQ ID NO:48).

Example 10 Identification of a Delta-9 Elongase From Euglena anabaenaUTEX 373

The present example describes the identification of delta-9 elongasesfrom a Euglena anabaena UTEX 373 cDNA library. This work is alsodescribed in U.S. Provisional Application No. 60/911,925 (filed Apr. 16,2007; Attorney Docket No. BB-1613).

Growth of Euglena anabaena UTEX 373 and Preparation of RNA

Amplified cDNA library eug1c was plated and colonies lifted as describedin Example 1. A DNA probe was made using an agarose gel purifiedNcoI/NotI DNA fragment containing the Euglena gracilis delta-9 elongasegene, from pKR906 (SEQ ID NO:42; Example 5 and WO 2007/061845, whichpublished May 31, 2007; Attorney Docket No. BB-1562 the contents ofwhich are hereby incorporated by reference) labeled with P³² dCTP usingthe RadPrime DNA Labeling System (Cat. No. 18428-011, Invitrogen,Carlsbad, Calif.) following the manufacturer's instructions.

Colony lifts were probed and positives were identified and confirmed asdescribed in Example 2. Plasmid DNA was isolated and sequenced exactlyas described in Example 1 and sequences were aligned and compared usingSequencher™ (Version 4.2, Gene Codes Corporation, Ann Arbor, Mich.). Inthis way, the clones could be categorized into one of two distinctgroups based on insert sequence (designated EaD9Elo1 and EaD9Elo2).EaD9Elo1 is also called EaD9e within but they are identical.Representative clones containing the cDNA for each class of sequencewere chosen for further study, and the sequences for each representativeplasmid (pLF121-1 and pLF121-2) are shown in SEQ ID NO:50 and SEQ IDNO:51, respectively. The sequence shown by a string of NNNN's representsa region of the polyA tail which was not sequenced. The coding sequencesfor EaD9Elo1 and EaD9Elo2 are shown in SEQ ID NO:52 and SEQ ID NO:53,respectively. The corresponding amino acid sequences for EaD9Elo1 andEaD9Elo2 are shown in SEQ ID NO:54 and SEQ ID NO:55, respectively.

Example 11 Construction of Soybean Expression Vector pKR1150 forCo-Expression of the Euglena anabaena UTEX 373 Delta-8 Desaturase(EaD8Des3) with a Delta-9 Elongase Derived from Euglena anabaena UTEX373 (EaD9Elo1)

The present Example describes construction of a soybean vector forco-expression of EaD8Des3 with EaD9Elo1.

In order to introduce NotI and NcoI restriction sites at the 5′ end ofthe coding sequences and a NotI site at the 3′ end of the codingsequences, EaD9Elo1 was

PCR amplified from pLF121-1 (SEQ ID NO:50; Example 10) witholigonucleotide primers oEAd9el1-1 (SEQ ID NO:56) and oEAd9el1-2 (SEQ IDNO:57) using the Phusion™ High-Fidelity DNA Polymerase (Cat. No. F553S,Finnzymes Oy, Finland) following the manufacturer's protocol. Theresulting DNA fragments were cloned into the pCR-Blunt cloning vectorusing the Zero Blunt PCR Cloning Kit (Invitrogen Corporation), followingthe manufacturer's protocol, to produce pKR1137 (SEQ ID NO:58).

EaD9Elo1 was released from pKR1137 (SEQ ID NO:58) by digestion with NotIand cloned into the NotI site of pKR72 (SEQ ID NO:43; Example 5) toproduce pKR1140 (SEQ ID NO:59).

Vector pKR1138 (SEQ ID NO:46; Example 5) was digested with BsiWI and thefragment containing EaD8Des3 was cloned into the BsiWI site of pKR1140(SEQ ID NO:59) to give pKR1150 (SEQ ID NO:60). A schematic depiction ofpKR1150 is shown in FIG. 11. In FIG. 11, EaD9Elo1 is called EAd9elong.

Example 12 Construction of an Arabidopsis Expression Vector pKR1192 forExpression of a Euglena anabaena delta-9 Elongase with a Euglenaanabaena delta-8 Desaturase

The AscI fragment of pKR1140 (SEQ ID NO:59; Example 11) was cloned intothe AscI fragment of pKR277 (which is described in PCT Publication No.WO 04/071467) to produce pKR1173 (SEQ ID NO:61).

The Gy1/Pavelo/legA2 cassette was released from plasmid pKR336(described in PCT Publication Nos. WO 04/071467; the contents of whichare hereby incorporated by reference) by digestion with PstI/BamHI andcloned into the PstI/BamHi site of pKR268 (described in PCT PublicationNos. WO 04/071467) to produce pKR393 (SEQ ID NO:62). The Pavelo gene wasreleased from pKR393 (SEQ ID NO:62) by digestion with NotI and thevector was re-ligated to from pKR407 (SEQ ID NO:63).

The NotI fragment from pLF120-3 (SEQ ID NO:30; Example 4), containingEaD8Des3 was cloned into the NotI fragment of pKR407 (SEQ ID NO:63) toproduce pKR1176 (SEQ ID NO:64).

The PstI fragment from pKR1176 (SEQ ID NO:64), containing EaD8Des3 wascloned into the SbfI fragment of pKR1173 (SEQ ID NO:160 61) to producepKR1178 (SEQ ID NO:65).

The AscI fragment of pKR1178 (SEQ ID NO:65), containing EaD9elo1 andEaD8Des3, was cloned into the AscI site of pKR92 (which was previouslydescribed in WO2007/061845 published on May 31, 2007 to produce pKR1192(SEQ ID NO:66). A schematic depiction of pKR1192 is shown in FIG. 12. InFIG. 12, EaD9Elo1 is called EA D9elong but they are identical. In thisway, EaD9Elo1 was expressed in Arabidopsis under control of the soybeanbeta-conglycinin promoter and the EaD8Des3 was expressed under controlof the soybean glycinin Gy1 promoter. The soybean beta-conglycininpromoter and Gy1 promoter function as a strong, seed-specific promotersin Arabidopsis.

Example 13 Functional Analyses of Delta-8 Desaturase in Soy

The present example describes the transformation and expression insoybean somatic embryos of pKR1152 (SEQ ID NO:47; Example 5) and pKR1150(SEQ ID NO:60; Example 11).

Soybean embryogenic suspension culture (cv. Jack) was transformed witheach of the vectors above and embryos were matured in soybeanhistodifferentiation and maturation liquid medium (SHaM liquid media;Schmidt et al., Cell Biology and Morphogenesis, 24:393 (2005)) asdescribed in Example 6 and previously described in PCT Publication No.WO 2007/136877, published Nov. 29, 2007 (the contents of which arehereby incorporated by reference).

After maturation in SHaM liquid media a subset of transformed soybeanembryos (i.e., 5-6 embryos per event) were harvested and analyzed asdescribed herein.

In this way, approximately 30 events transformed with either pKR1152(SEQ ID NO:47; Example 5; called Experiment MSE2136) or pKR1150 (SEQ IDNO:60; Example 11; called MSE2130) were analyzed and the five eventshaving the highest average DGLA content (average of the 5 embryosanalyzed) are shown in FIG. 3 or 14, respectively. In FIGS. 3 and 14,fatty acids are identified as 16:0 (palmitate), 18:0 (stearic acid),18:1 (oleic acid), LA, ALA, EDA, ERA, DGLA and ETA. Fatty acidcompositions are expressed as a weight percent (wt. %) of total fattyacids.

In FIGS. 3 and 14, elongation activity is expressed as % delta-9elongation of C18 fatty acids (C18% delta-9 elong), calculated accordingto the following formula: ([product]/[substrate+product])*100. Morespecifically, the combined percent elongation for LA and ALA isdetermined as: ([DGLA+ETA+EDA+ERA]/[LA+ALA+DGLA+ETA+EDA+ERA])*100.

In FIGS. 3 and 14, the combined percent desaturation for EDA and ERA isshown as “020% delta-8 desat”, determined as:([DGLA+ETA]/[DGLA+ETA+EDA+ERA])*100. This is also referred to as theoverall % desaturation.

Example 14 Functional Analysis of Arabidopsis Seed Transformed withpKR1192 for Expression of a Euglena anabaena delta-9 elongase with aEuglena anabaena delta-8 desaturase in Arabidopsis

A fad3/fae1 double mutant (Smith et al., Planta 217:507-516 (2003)) ofArabidopsis produces seed where the ALA and 20:1 fatty acid content isless than 2.0%. The fad3/fae1 double mutant Arabidopsis plants weretransformed with pKR1192 (SEQ ID NO:66), and plants were grown,maintained and seed was harvested as previously described in WO2007/061845 (the contents of which are hereby incorporated byreference).

Segregating T2 seed was obtained from 21 individual events for each andbulk T2 seed lipid profiles for each event were obtained bytransesterification with TMSH as described in herein with the followingmodificiations. For each event, a small scoopful of seeds (approximately25-50 seed each scoopful) was crushed in 50 μL of TMSH in a 1.5 mLeppendorf tube. After shaking in TMSH for 15 min., 400 μL of heptane wasadded and the tubes were vortexed well, shaken for an additional 15 minand centrifuged at 13,000×g for 1 min. After shaking, the heptane layerwas removed into glass GC vials and the fatty acid methyl esters wereanalyzed as described in herein.

The lipid profiles of T2 bulk seed for the 21 transformed events isshown in FIG. 15. Fatty acids are identified as 16:0 (palmitate), 18:0(stearic acid), 18:1 (oleic acid), LA, ALA, 20:0 (eicosanoic acid), 20:1(eicosenoic acid), EDA, DGLA, ERA and ETA; and, fatty acid compositionslisted in FIG. x5 are expressed as a weight percent (wt. %) of totalfatty acids.

In FIG. 5, the combined percent desaturation for EDA and ERA is shown as“020% delta-8 desat”, determined as:([DGLA+ETA]/[DGLA+ETA+EDA+ERA])*100. This is also referred to as theoverall % desaturation.

1. An isolated polynucleotide comprising: (a) a nucleotide sequenceencoding a polypeptide having delta-8 desaturase activity, wherein thepolypeptide has at least 80% amino acid identity, based on the Clustal Vmethod of alignment, when compared to an amino acid sequence as setforth in SEQ ID NO:21, SEQ ID NO:22, SEQ ID NO:23 or SEQ ID NO:24; (b) anucleotide sequence encoding a polypeptide having delta-8 desaturaseactivity, wherein the nucleotide sequence has at least 80% sequenceidentity, based on the BLASTN method of alignment, when compared to anucleotide sequence as set forth in SEQ ID NO:17, SEQ ID NO:18, SEQ IDNO:19 or SEQ ID NO:20. (c) a nucleotide sequence encoding a polypeptidehaving delta-8 desaturase activity, wherein the nucleotide sequencehybridizes under stringent conditions to a nucleotide sequence as setforth in SEQ ID NO:17, SEQ ID NO:18, SEQ ID NO:19 or SEQ ID NO:20; or(d) a complement of the nucleotide sequence of (a), (b) or (c), whereinthe complement and the nucleotide sequence consist of the same number ofnucleotides and are 100% complementary. 2-38. (canceled)
 39. Thepolynucleotide of claim 1 wherein the nucleotide sequence comprises SEQID NO:17, SEQ ID NO:18, SEQ ID NO:19 or SEQ ID NO:20.
 40. Thepolynucleotide of claim 1, wherein the amino acid sequence of thepolypeptide comprises (a) SEQ ID NO:21, SEQ ID NO:22, SEQ ID NO:23 orSEQ ID NO:24; or (b) an amino acid sequence that differs from the aminoacid sequences in (a) by at least one conservative amino acidsubstitution.
 41. A recombinant DNA construct comprising thepolynucleotide of claim 1 operably linked to at least one regulatorysequence.
 42. A plant cell comprising in its genome the recombinant DNAconstruct of claim
 41. 43. A method for producing a transformed plantcomprising transforming a plant cell with the polynucleotide of claim 1and regenerating a plant from the transformed plant cell.
 44. Atransgenic seed comprising in its genome the recombinant construct ofclaim
 41. 45. A transgenic seed obtained from the plant made by themethod of claim
 43. 46. Oil or by-products obtained from the seed ofclaim
 44. 47. A method for making long-chain polyunsaturated fatty acidsin a plant cell comprising: (a) transforming a cell with the recombinantconstruct of claim 41; and (b) selecting those transformed cells thatmake long-chain polyunsaturated fatty acids.
 48. A method for producingat least one polyunsaturated fatty acid in an oilseed plant cellcomprising: (a) transforming an oilseed plant cell with a firstrecombinant DNA construct comprising an isolated polynucleotide encodingat least one delta-8 desaturase polypeptide, operably linked to at leastone regulatory sequence and at least one additional recombinant DNAconstruct comprising an isolated polynucleotide, operably linked to atleast one regulatory sequence, encoding a polypeptide selected from thegroup consisting of a delta-4 desaturase, a delta-5 desaturase, adelta-6 desaturase, a delta-8 desaturase, a delta-12 desaturase, adelta-15 desaturase, a delta-17 desaturase, a delta-9 desaturase, adelta-9 elongase, a C_(14/16) elongase, a C_(16/18) elongase, aC_(18/20) elongase and a C_(20/22) elongase; (b) regenerating an oilseedplant from the transformed cell of step (a); and (c) selecting thoseseeds obtained from the plants of step (b) having an altered level ofpolyunsaturated fatty acids when compared to the level in seeds obtainedfrom a nontransformed oilseed plant.
 49. The method of claim 48 whereinthe oilseed plant is selected from the group consisting of soybean,Brassica species, sunflower, maize, cotton, flax, and safflower.
 50. Anoilseed plant comprising: (a) a first recombinant DNA constructcomprising an isolated polynucleotide encoding at least one delta-8desaturase polypeptide, operably linked to at least one regulatorysequence; and (b) at least one additional recombinant DNA constructcomprising an isolated polynucleotide, operably linked to at least oneregulatory sequence, encoding a polypeptide selected from the groupconsisting of a delta-4 desaturase, a delta-5 desaturase, a delta-6desaturase, a delta-8 desaturase, a delta-12 desaturase, a delta-15desaturase, a delta-17 desaturase, a delta-9 desaturase, a delta-9elongase, a C_(14/16) elongase, a C_(16/18) elongase, a C_(18/20)elongase and a C_(20/22) elongase.
 51. The oilseed plant of claim 50,wherein the oilseed plant is selected from the group consisting ofsoybean, Brassica species, sunflower, maize, cotton, flax and safflower.52. A transgenic seed obtained from the oilseed plant of claim
 50. 53.Oil or by-products obtained from the seed of claim
 52. 54. Oil obtainedby the method of claim
 47. 55. Food or feed which incorporates the oilof claim
 53. 56. Food or feed which incorporates the oil of claim 54.57. Food or feed comprising the seed of claim
 52. 58. Food or feedcomprising an ingredient derived from the processing of the seeds ofclaim
 52. 59. The oil or by-products of claim 53 wherein the by-productis lecithin.
 60. A method for making long-chain polyunsaturated fattyacids in a plant cell having a reduced level of by-product fatty acids,said method comprising: (a) transforming a plant host cell with at leastone recombinant DNA construct comprising an isolated polynucleotideencoding at least two delta-8 desaturases operably linked to at leastone regulatory sequence; and (b) selecting those transformed plant hostcells obtained having a reduced level of by-product fatty acids, whencompared to the level of such metabolic by-product fatty acids in atransformed host cell having at least one recombinant DNA constructcomprising an isolated polynucleotide encoding one delta-8 desaturaseoperably linked to a regulatory sequence.
 61. Progeny plants obtainedfrom the plant made by the method of claim
 43. 62. Progeny plantsobtained from the oilseed plant of claim 50.